3 Days in Nagasaki: My favourite Nagasaki itinerary

I have been singing the praises of Nagasaki elsewhere, so this post is going to be more practical and will give you a sensible yet fun Nagasaki itinerary.

Most visitors to Japan don’t even make it to Kyushu, and those those who do tend to make a day trip to Nagasaki. When I read my Japan guidebook, I remember reading that of all the cities in Kyushu, Nagasaki has a bit of everything – history, scenery, food, nature. So, if you were to visit just one city in Kyushu, Nagasaki might be most suitable.

But… There is a catch. I can give you the nicest Nagasaki itinerary, but the city is not super accessible. The largest city of Kyushu, Fukuoka, sits at the north of the island and is the terminus of the Hakata Shinkansen. From here, you can easily continue to Kumamoto and Kagoshima on the Kyushu Shinkansen .

Nagasaki? Argh, it’s a bumpy ride. I travelled late at night, hungover from 35 hours of travelling, somewhat in a rush to check in at my hotel before midnight. I’d been dragging my luggage onto the metro and into Hakata Station, hastily purchased a ticket for the last train and endured a bumpy Kagome relay train ride before finally boarding the nice Nishi-Kyushu Shinkansen at Takeo Onsen for the final 20 minutes. I reached Nagasaki shortly before midnight. On these first couple hour sin Japan, I also encountered the only rude person in six weeks in Japan: a train conductor shouting at me for sitting in a reserved carriage on an empty Kagome train. It was swerving and bumping so badly,  I had real trouble transferring myself and my luggage into the unreserved carriage for the 20 minutes that remained.

This encounter cured me of Japan Rail for six weeks. I gingerly stepped back on (superb) local trains in the last week of my stay. However the highway bus to Fukuoka was a much better experience at a third of the price of the train ticket. Only six weeks later did I set my foot on a local train.

But once you arrive in Nagasaki, it’s wonderful and you might not want to leave. Local transport is easy and cheap. Which is good – Nagasaki is quite hilly and walking can be exhausting, so tram, buses and locals trains are a good way to get around. I hope you enjoy this Nagasaki itinerary.

So, here’s a nice three-day Nagasaki itinerary. Please stay longer if you can. I think, with side trips like Arita for some ceramics shopping and the stunningly beautiful Okawachiyama, a trip to Shima-Hanto and an onsen and a beach day or two, you can easily spend  a week or two in Nagasaki.

Nagasaki itinerary Day 1:  Arrive, walk to temples, enjoy the Mount Inasa Night View

My Nagasaki itinerary starts at the JR (Japan Rail) Station. This is the central arrival point for trains, highway buses and the airport bus. Like many large train stations in Japan, it’s fairly nice, clean and has a huge food court with a souvenir mall. So, you can stop here for a pretty decent meal right after arriving. There are also coin lockers for your luggage. Some of the larger hotels will store luggage, too; most operate fairly strict afternoon check-in times.

Depending on where you are staying, take a walk through the local neighbourhood, and take note of nearby convenience stores. Crowds will disperse as soon as you leave the JR Station area.

Convenience stores in Japan are great  – food often is high quality, and they even sell basic clothing! I have bought complete dinners there, frozen edamame, fresh noodles – the vast array of foods squeezed into these tiny spaces is baffling. Also, many have a cash machine. I found that the Lawson Station ones worked well with my German credit card for cash advances.

The best way to get around Nagasaki is by tram. You will probably see museum-quality single tram cars moving through the streets – these are public transport, not for sightseeing, and people use them a lot. Nagasaki is hilly, and the trams basically move in the valleys around the city. Their rolling stock is true vintage, with a few low floor newer models. I really admire  the dedication that goes into maintaining these nice trams cars.

Once you have gotten to know your local area, consider visiting a temple or shrine. The hillside around the centre is dotted with them. I have a few on this Nagasaki itinerary that are really worth a detour.

I would say the most famous shrine in Nagasaki is the Suwa-Jinja, a shrine in the north of the city centre. It has its own tram stop, so very easy to get to.

The shrine is a proper old one and dates back to the early 17th Century – a period when the ruling shogunate issued edicts against Christians, and served to position the shogunate and shinto as a major religion against a Christian majority in Nagasaki. The shrine was spared by the bomb, due to its sheltered location in a hillside. The approach on some wide stone steps is lovely, and the shrine, despite its popularity is not crowded for all but a few days in Autumn when the famous Nagasaki Kunchi Matsuri is held.

Then walk past the park and the Museum of History and Culture, which makes a great rainy day option,  towards the train station. the whole area is residential and has some great architecture. Staying in the Western part of central Nagasaki, just continue to wander.

Kamimachi-Dori leading from the museum towards the JR Nagasaki Station has a mixture of venerable old wooden houses mixed with quietly elegant concrete dwellings. A couple streets further up, Shofuku-ji is a magnificent old Buddhist Temple,, where renovations works should be finished by now. Another noteworthy temple along the road is Fukusai-ji, a 1970’s recreation in the shape of a giant turtle with a huge Kannon statue riding on it. These are just a few – the entire street is lined with temples.

If you are on the Southeastern side of the centre, then head towards Kofukuji Temple. This is one of the city’s oldest Buddhist temples, founded by a Chinese monk, at a time when trade with China was flourishing.

Continue along Teramachi, a quiet residential street, which is dotted with temples and shrines. If your feet will carry you, walk as far Sofukuji and Kiyumizudera. About halfway, near Hamamachi Arcade, you will find a cluster of nice small cafes and restaurants.

When you cross the town centre on foot, you will cross some nice hills, lovely exercise. Make sure you walk across the Megane Bridge, one of Japan’s oldest stone bridges (built in the 17th century) , at some point. The Meganebashi area is really lovely, urban, but many pedestrian areas, small cafes and pubs. The somewhat retro chic Hamamachi Shopping Arcade is less than 5 minutes walk from here.

When you are done with enough temples, head for one of the world’s nicest “night views”. Just make sure that you leave enough time to go up Mount Inasa, from where you will have a magnificent view over the Nagasaki Hills and Nagasaki Bay. The easiest way to get there is by tram 1 or 3 to Takaramachi Station, cross the river on foot then take a cable car.

This is the one thing I regret not doing – the cable car was on its annual service, and after half an hour trying to catch the bus up, I gave up! So, there are buses going up there, but they are a bit difficult to identify if you’re unable to read Japanese.

Day 2:  Northern Nagasaki Atomic Bomb Memorials and Mihara Gardens

Now you have gotten your bearings on the city’s layout, you can head north to the suburb of Urakami.

Nagasaki is the second and hopefully the last city to ever be hit by a nuclear bomb, and the memory lives on with references everywhere in town. The memorials are somewhat different to Hiroshima. It makes sense to start at the Hypocentre Park, which is peaceful yet very informative.

Move on to the Peace Park, a very large statue-filled park that sees many visitors, including the cerulean blue Peace Statue that certainly divides opinion.

From here, you can go and visit some of the minor memorials, like the Nyoko-do Hermitage (my personal favourite), or the Nagasaki Medical College (now University of Nagasaki Sakamoto Campus). 

Another really nice short walk leads you up some stairs past the one-legged torii which survived the bomb, up to Sanno Shrine which was reduced to rubble, except for two mighty camphor trees, which also survived.

You’re unlikely to find other tourists here, it’s a very lovely residential area.

Of course, the nearby Atomic Bomb Museum is where most visitors go. It is very good, relatively small, and an hour is plenty. In terms of the quality of the museum only, I think Hiroshima does it better. But then, the Nagasaki Atomic Bomb memorials are more than the museum, and there are plenty of options to learn.

End the day on a cheerful note. You want to return to the Atomic Bomb Museum tram stop, take a bus or taxi from there to Mihara Gardens, about 15-25 minutes away, up in the Nagasaki Hills. If you are a garden nut like me, plan to spend three hours there. The gardens are relatively small but growing, with many different zones tucked into a hillside, a work of Kazuyuki Ishihara, a Nagasaki native.

The Kawaguchimachi/Hamaguchimachi area to the east between the Atomic Bomb Museum and Urakami Station tram stops is great for food and drinks in the evening, or you can also return to the centre.

And that’s your second day on this Nagasaki itinerary completed.

Day 3: Dejima and  Meiji Industrial Revolution Sights

Today on our Nagasaki itinerary, let’s stick a little closer to the centre, maybe shop a little before moving on.

Dejima, a historic Portuguese, then Dutch Trading post, is very close to Nagasaki station and, going forward in history, your first port of call. It was once an island and a small town in its own right, shut off from the rest of Japan due to the “sakoku”, the seclusion policy imposed by Shogunate rulers. It is now a pretty open air museum, with reconstructed traditional houses from its “Durch” period engulfed by nondescript downtown concrete.

Move on to the port area where you will find Glover Gardens, Oura Cathedral and the Gunkanjima Digital Museum.

I would say this is Nagasaki’s most touristy area, especially the small street leading up to Oura Cathedral is lined with souvenir shops and can get very full.

Oura Cathedral is Japan’s oldest church and charges a hefty entrance fee, but certainly pretty to view from outside. If you wish to learn about Christianity in Japan, the Museum of 26 Martyrs,a short walk up from the train station might be a better (and suitable rainy weather) option.

In good weather, continue to Glover Gardens, a huge park with some mid-19th Century residences built by Western merchants, affording great views over the city and the Mitsubishi shipyards.

The main highlight for me was the Nagasaki Traditional Performing Arts Center inside the gardens, which shows some of the floats and portable shrines from the Nagasaki Kunchi Festival.

If crowds aren’t your thing, consider the nearby Nagasaki Koshibyo Confucius Shrine and Historical Museum of China, a colourful shrine out front and modern culture museum at the back.

If you have more time and the weather is favourable, you can visit the now famous Hashima Island, colloquially called Gunkanjima. It was a coal mine for nearly a century and was once one of the densest inhabited places on earth. These trips are fairly pricey (3600JPY/22 Euro if booked directly, about 36 Euro if booked through a third party like Klook) and if you land, then you can move about 200m into the islands in a designated area – this is the main reason why I didn’t go. Often, sea conditions are less than great, so the boats to a trip round the island.

If that’s too much of a gamble, there is the Gunkanjima Digital Museum near Glover Gardens, ideally visited before the cruise or on its own.

Wind down in Chinatown or Shianbashi with a drink and dinner to conclude your Nagasaki trip.

Where to stay in Nagasaki

Nagasaki is full of hotels and inns, most belonging to local or national chains. The most convenient area to stay is the JR Nagasaki Station. If you love nightlife, Shinchi Chinatown is your place to stay.

The perfect balance of all is the lovely residential area between the Nagasaki Museum of History and Culture and the train station. Easy to walk, or two stops on the tram. This area, called Tamazonomachi is my favourite area of Nagasaki. You can walk to the station in 10 minutes, or go by tram (Sakuramachi) in 5 minutes, and it’s in a nice residential area.

Shindaikumachi and Sakurababa a bit further out are also really nice. Basically, anything on the No. 3 Tram between JR Train Station and Hotarujaya is good.

Also, the area between the Atomic Bomb Museum and Urakami Station is a fairly good and relatively cheap area to stay, full of little restaurants and bars and quite atmospheric. Most hotels will be around the train station, and they’re okay, but it’s definitely more urban, less atmospheric.

I will give you a few recommendations – most places I stayed in myself, some are places where classmates stayed, some I went to check out. It’s a rather small selection, tried and tested.

Chic Minimalist Style: Grand Base Nagasaki City

Grand Base was my first “home away from home” when I went on my course in Nagasaki. I wanted comfort and Western Style, and good access to the tram. For less that 300 Euro per week, I got a spacious one-room apartment with kitchenette, a huge bathroom with a washing machine, all new, in a super quiet location yet only five minutes walk from the nearest tram stop.  The building is a new low-rise and has maybe 20 units.

My apartment had two very large beds, making this a good choice for up to four people, a sofa and coffee table and lot of space. Although I missed a desk, it was comfortable for studying. I also could make my own breakfast and dinner easily, thanks to a well equipped kitchenette.

Beds were super comfy, it was really clean.  Style is minimalist Western style except for the bath setup and the all-singing and dancing toilet in its own palatial room. The only hiccup was it is an unstaffed property and I arrived late at night… self-check-in was a bit of faff, but there was a phone to get assistance, and it all worked out. Once checked in, it was easy to communicate by messaging. For a very comfortable stay in a nice residential area, I really recommend Grand Base Nagasaki City.

Another of their hotels, Grand Base Nakamachi, is located even closer to the station and is very similar.

Tradition in the city: Relaxing Inn Origami  (和みの宿 おりがみ)

Origami Inn down the road from Grand Base is the choice for travellers who prefer a bit more “traditional Japanese style”. The inn is in a small modern building, with just a few rooms. The first floor has a small cafe and bar and some Western Style rooms, whereas the second floor has tatami rooms and it a lot more Japanese in character down to the corridor and huge family bath.

I stayed two weeks in this place. My room, a spacious tatami room, was very traditional Japanese in style – low tables and legless chairs and all. Sleeping on the tatami floor on a classic (thin!) futon set-up took a bit of adjustment. But for the authentic Japanese experience, it was well worth it. The room had a small fridge as well.

The communal area has a huge bath, sinks, a microwave, kettles and water dispensers.

The cafe was usually empty, but the staff take great price in it, and roast their own coffee, which they will happily supply in neat little packets for breakfast. Another big plus was the ample private off road parking space which cost just 500 JPY a day. So, if you bring your car into the city, and want a very Japanese experience in central Nagasaki, try the Relaxing Inn Origami. I paid about 600 Euro, just for myself, for just under two weeks.

Business Hotels: Plain, Comfy and Central

Like in all larger towns of Japan, Nagasaki has business hotels aplenty. I picked the SPeria Hotel Nagasaki for location and price (around 40 Euro per night) and was not disappointed. It is one of the typical Japanese convenient, lower priced business hotels. It is quite conveniently located 150 metres from a tram stop, 120 minutes walk from the train station and right by a main road. The area isn’t charming, but you are certainly very central, and one of my favourite restaurants (Hiroshimatei) and coffee shops (Kariomon) are literally next to the hotel. There’s three shopping malls in walking distance, and you can walk to almost all central Nagasaki sights from here.

What’s not to love? Honestly, as far as business hotels go, you could not do much better. I paid around 40 Euro per night for a double room with single occupancy. It was newly furnished, comfortable, and I finally had a desk! Okay, a small one, and barely room for anything else, but  the room got serviced daily, we had a microwave (in the lobby, of all places) , cheap self service laundry, and a super comfortable bed and a bit of built in storage. Not ideal when you have just bought a huge box of porcelain, your husband notoriously overpacks, and you have luggage worth six weeks and a fair bit of shopping, but Japanese rooms are known to be small, and this wasn’t the smallest room I stayed in.

Every one might have their favourites – Toyoko Inn is best-known outside Japan but fairly basic, Dormy Inn has an on-site onsen bath, and for the four-star experience, the Candeo Hotel Nagasaki Shinchi Chinatown offers unbeatable value, but the SPeria Hotel suited my needs perfectly.

Lovely on a budget: Himawari Hotel

Last not least: one of my favourites. In terms of value for money, this is high above everything else here. Yes, it is spartan. But it’s clean, spacious, there is a tram stop and tons of little restaurant just outside the door, and there is a communal kitchen. The photos do it no justice.  I really didn’t expect much but six weeks in Japan, tuition fees and airfare were eating up my budget. Plus I wanted to be near the university for the last two weeks of my course and expected to study a lot, so I booked this small hotel.

When I entered my single room, I was pleasantly surprised. Huge by Japanese standards, bright, with a comfortable double bed and a small desk and small shelf. The aircon was working. It was spotlessly clean.

Honestly, I didn’t need more, Thanks to a good supermarket with the most extensive deli and the use of a shared kitchen, I would often eat at home, but there probably hundred restaurants in a the grid of small streets just outside the door.

The place is run by the loveliest couple ever. They do everything to accommodate you.

The Atomic Bomb Museum ist 5 minutes on foot, the University Hospital and Medical School are about 5-10 minutes on foot. I did not find anything comparable for roughly 20 Euro per night for a private room, so  Himawari Hotel  is my budget recommendation.

This was by far the cheapest budget accommodation with a private room. Another good choice in the Atomic Bomb Museum area is Mezame Hostel which has both dorms and private rooms. For budget accommodation in the centre, try ROUTE-Cafe and Petit Hostel – they have semi-private bunks in their dormitories and some private family rooms and location is unbeatable – opposite a park yet less than 5 minutes walk from the Nagasaki Train Station.

Side Trips and alternative options

As someone who’s stayed in Nagasaki for six weeks, I would recommend a week as a good period to spend in and around Nagasaki.

I am going to keep this fairly short and just list some ideas for day trips or short overnight trips, some of which I have already posts up.

If you have a rainy day or just want some rest, I recommend one of Nagasaki’s onsen. Fuku no Yu is the easiest accessible one with a free shuttle from various places in the city, and very cheap yet offering a huge range of different bathing options.

I also did a day trip to Arita, where I participated in Kouraku Kiln’s Arita Treasure Hunt, and visited the scenic ceramicist village of Okawachiyama.

I also drove all over Saga prefecture all the way to Itoshima peninsula, with scenic forests, cool paper workshops, a traditional salt maker and the lovely under-visited little town of Karatsu, all in one day.

Last not least, the Mt. Unzen area, with its active volcano, onsen galore and the delightful town of Shimabara are also well worth a visit.

And there’s more – I just did not manage to visit it all in six weeks!

Where to eat

This might actually go beyond the scope of this post, so I might write another post on eating in Nagasaki, about regional foods and my favourite restaurants…

Generally speaking, Nagasaki is a great city for food. While there are quite a few tourists, they spread quite nicely over the city centre, so while you might  get some meh restaurants round the train station and in the malls there, it’s quite easy to find great food in Nagasaki.

My favourite areas for really good local food are around Siebold Street (Shindaikumachi), the Hamanomachi area and  Hachiguchimachi, north of Urakami Station.

My all-over favourite was Hiroshimatei, an okonomiyaki restaurant near Gotomachi tram stop. Small, family-owned, with a nice mix of locals and the odd tourist. Very reasonably priced alcoholic drinks, too.

Another place I liked is Mutsugoro, a short walk from Shindaikumachi tram. Described as “Izakaya” this is actually a large restaurant offering fresh seafood at very reasonable prices. And speaking of sushi, Sushi Shippoku Katsura (すし·しっぽく かつら, Plus Code QV3Q+82 Nagasaki, Präfektur Nagasaki, Japan ) is even more cosy and simply had the best sushi I tried in Nagasaki, but also some other dishes.

If speaking Japanese is not your thing, Dejima Wharf has a few nice well-rated options where English is spoken as it’s a fairly touristy area.

What to Eat

Nagasaki is famous for Chinese food, creamy noodle soup called Champon, and for Castella cake, an imported concoction not dissimilar to a pound cake, but lighter and with typical Japanese flavours. .

Well. I give the first one a pass, being mostly vegetarian, definitely not eating meat. I tried Castella cake, which is basically a European-style, very sweet and fluffy pound cake. My mate said his granny would make a better one. It was fine but… back to the mochi and green tea everything it was.

So while I wasn’t so keen on Nagasaki’s famous food products, I found some really fresh sushi, really nice comfort food and just really good standard Japanese food.

And, to be honest, I wanted sushi. Super fresh fish, expertly prepared, and then, after three or four fishy meals, I switched to vegetarian sushi, of which there usually is plenty.

The Small Print

I studied in Nagasaki in May 2023. This Nagasaki Itinerary is a condensed version of my weekend sightseeing over six weeks. As always, I have no sponsorship, all expenses were paid by myself, all unbiased reviews. The accommodations links are affiliate links to Booking.com.

If you have any questions about onsen or Nagasaki, feel free to drop me a line or comment. I spent six week in Nagasaki so I know the city fairly well from a tourist point of view now.

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