What is Beyond Tokyo and Kyoto: My Three Favorite Cities in Japan

Considering it is now almost the spring season—the perfect time for urban travels—it may be a good time to talk about “other” cities in Japan that are worth a visit and which are not Tokyo or Kyoto.

In this post, I will introduce you to three of my favorite cities in Japan, which are all rich in terms of sites shining a light on the historical events and movements that shaped the present day Japan. One of these cities is already very well known for both pleasant and tragic reasons, while the other two still remain relatively undiscovered by international visitors. But I vouch for each of them as a wonderful urban travel destination.


Nagasaki: one of the first cities in Japan to embrace the outside world

Last Sunday, on the day that Oppenheimer got the Oscar for the best movie, I was in Nagasaki visiting the Atomic Bomb Museum. With the displays realistically depicting the event, explanations not holding anything back, and particularly the Remembrance Hall, visiting the Nagasaki Atomic Bomb Museum is always a deeply sorrowful experience.

Remembrance Hall in Nagasaki Atomic Bomb Museum, March 2024.

I find Nagasaki to be one of Japan’s most important cities to visit. It offers profound insight into the country’s historical interactions with the outside world that helps to put modern-day Japan and how it sees the outside world in a better context. While the city is ingrained in our global consciousness with the horrific event of August 1945, ironically, centuries before the atomic bombing, Nagasaki was one the first places in Japan to open its doors to Western culture.

Following the arrival of Portuguese ships on the Japanese shores in the 16th Century, the city quickly became the center of international trade. The ships brought not only tradable goods but also a heavy Western influence, particularly religion. The Christian (mainly Catholic) influence in the city was so strong that Nagasaki was referred to as “Little Rome” at the time.

Oura Church in Nagasaki.

However, following a brief period of openness, free trade, and cultural exchange during which Nagasaki played a front and central role, Japan entered the Sakoku period (meaning locked country) in 1639. During this lengthy period, which lasted until 1853, most foreigners were banned from entering the country while the Japanese were kept from leaving Japan. The policy also entailed a ban on Christianity. But even during this period, Nagasaki remained the only port in Japan open to foreign trade, but in a rather strange manner.

A (fan-shaped!) artificial island called Dejima was constructed off Nagasaki City in 1636, shortly before the beginning of the Sakoku Period. While the small island was initially used to host the Portuguese traders and keep them segregated from the Japanese public (due to, at the time, un-welcomed religious influence), it soon became the home of Dutch merchants, the only western group allowed to enter and trade in Japan during the Sakoku Period.

Dejima was home to around 10 to 20 Dutch trade workers, who were not allowed to leave the island except for very limited circumstances, along with some Japanese officials and around 40 buildings, including residences, offices, and warehouses. Dejima, which had once been connected to the mainland with a bridge guarded on both ends, is no longer an island. The surrounding marine area had been reclaimed during the Meiji Period. Today, the island, a mere 15-minute walk from the train station, is open to visitors.

The allure of Nagasaki is not only about these historical sites. Despite the heavy past, Nagasaki is also one of the liveliest cities in Japan. Embraced by the narrow Nagasaki Bay, it is one of those cities softened by the sea where the water evokes a delightful sense of carefreeness. Surprisingly, there are “even” cafes and restaurants right by the water where people watch the busy harbor traffic and enjoy a morning coffee or an afternoon drink—a rarity in Japan despite it being an “island nation” where there is usually a barrier/road/tetra paks between the inland life and the sea.


Hirosaki: a city that escaped air raids during WW II

While Nagasaki played a crucial and progressive role in Japan’s interactions with the Western world in the 16th Century, Hirosaki, a northern Japanese city located in Aomori Prefecture, is also known for its openness to the Western culture, but for the events that occurred centuries later during the Meiji Restoration Period.

A coffee house in Hirosaki.

The Meiji Restoration, which started in 1868 following a lengthy period of self-imposed isolation during the Edo Period, aimed for a modernized and industrialized Japan. The city took the restoration policies of the time to heart and invited teachers, technical experts, and artists from the United States and Europe to speed up the integration into the world. Hirosaki, which also avoided air raids during World War II, is known today for its abundance of Western-style architecture, which has remained intact since the Meiji Period. The Western influence is also reflected in the city’s dining scene, with many restaurants serving European cuisine.

Hirosaki Castle Park.

Besides the Meiji Period architecture, another big draw of Hirosaki is the Hirosaki Castle, one of the only 12 castles in Japan that remain in their original form since the Edo and earlier eras. The castle, a reminder of the city’s feudal past, is surrounded by a magnificent park, which, to be honest, excited me even more than the castle (granted, this was due to the fall foliage).

If you ever make it to Hirosaki, I also highly recommend the Museum of Contemporary Art. The museum occupies an old, stylish brick building that used to be a brewery during the Meiji Period. They launch two exhibitions per year featuring artists who highlight the culture of Hirosaki and Tohoku. On the premises, there is a library, studio space, and a cafe (offering happy hours featuring the cider made with apples that the region is famous for).


Matsumoto: the hometown of Yayoi Kusama

Matsumoto, a mid-size town in Nagano prefecture, is one of those little gems of a city that punch above its weight when it comes to visitor attractions.

The city, just like Hirosaki, is home to one of the original 12 castles of Japan. Referred to as Crow Castle (Japanese love to nickname their castles) due to its black exterior, the castle’s main keep is still in its original form, built in the 16th Century.

The similarities between Matsumoto and Hirosaki are not limited to their original castles. Both cities are excellent representations of an aspect that I deeply appreciate about Japan—how modern-day life perfectly blends in with and complements the city’s historical attractions and its traditional culture.

Lucky for Matsumoto, the city is also the birthplace of the renowned Japanese artist Yayoi Kusama. Thanks to the generosity of Kusama, the Matsumoto City Museum of Art exhibits a reasonably large collection of her work. The collection of the artist’s work on permanent display in the museum, titled The Place for My Soul, includes a series of canvas paintings, polka dot walls, the famous pumpkin, and infinity rooms Kusama is most well-known for. 

Kusama’s art, which offers the viewers an immersive experience, is known to draw large crowds (for example, in Tokyo, the Yayoi Kusama Museum requires advance booking). However, on the day I visited the Matsumoto City Museum of Art, there were, despite the national holiday, only a few visitors besides me, making the experience feel almost like a private viewing. So, if you are a fan of her work, in addition to other attractions, the museum may be a reason alone to visit Matsumoto (which takes around 2.5 on the express train from Tokyo).

Last but not least, Matsumoto is also the getaway to one of Japan’s most picturesque nature areas, Kamikochi, and to the most visited postal towns of the Nakasendo Route, the historical route that connected Tokyo to Kyoto during the Edo Period via 69 postal towns—both accessible within an hour.


These are some of my favorite cities in Japan, which I believe are all worthy of that detour from Tokyo and Kyoto.

P.S: This was a shorter version of the March edition of the Letters from Japan that I e-mail once a month. Here is the full copy Letters from Japan, March 2024.


Are you looking for more places to visit in Japan?

You can start with my Japan travel guide here.

If you are not short on time, there are countless other destinations in Japan. Getting off the mainland to visit the smaller islands is a wonderful option to experience the “extremely” rural life centered around the ocean. These are some of my favorite islands in Japan.

If you like hiking, you are in luck. Mountains cover 70% of Japan`s land, and host thousands of trails fit for both beginner and advanced hikers, these are some of the hikes in Japan easily accessible with public transportation.

To experience the famous onsen (hot springs) culture of Japan, you can check out my post where I listed some of my favorite onsen in Japan.

If you visit Japan during the fall colors season, these are some of my favorite fall foliage viewing destinations in the country.