Tokyo, Kyoto, and Osaka get most of the attention — and honestly, they deserve it. But Japan is one of those rare countries where the further you stray from the obvious choices, the better things get.
The secondary towns scattered across the country are where you find the real texture of Japanese life: the ancient castles that survived the wars, the hot spring towns that have barely changed in centuries, and the regional food scenes that locals are quietly proud of.
Here is a list of 16 secondary towns that deserve a serious place on any Japan itinerary. Each one brings something genuinely different to the table.
Kanazawa
Kanazawa is a Sea of Japan coastal city that’s often referred to as “Little Kyoto,” but the locals probably wouldn’t appreciate the comparison. They have one of Japan’s three great gardens, a lovely old samurai and geisha district, and a fish market, Omicho, that gives the former Tsukiji Market a run for its money.
Kanazawa was also mercifully untouched by World War II bombing, which explains why the old town feels like a step back into the past.
Matsumoto
Matsumoto is home to one of Japan’s most striking original castles — a black-and-white fortress nicknamed ‘Crow Castle’ that dates back to the late 16th century. The town sits in the Japanese Alps at around 1,800 feet above sea level, which means the air is clean, the views are dramatic, and the summers are milder compared to Japan’s coastal heat.
It is also a practical base for exploring the mountain resort town of Kamikochi, just 90 minutes away.
Takayama
Tucked deep in the mountains of Gifu Prefecture, Takayama is the kind of place that rewards slow travel. Its Sanmachi Suji district — a row of well-preserved Edo-period merchant houses — is genuinely photogenic in a way that does not require much imagination.
The town is also famous for its twice-yearly festivals, considered among the most beautiful in Japan, and for Hida beef, a local wagyu variety that rivals anything Kobe produces.
Beppu
Beppu, on the island of Kyushu, is Japan’s hot spring capital in the most theatrical sense of the word. The city produces more geothermal water than almost anywhere else on earth, and you can feel it — steam drifts up from drains, gutters, and roadside vents throughout the city like something out of a fantasy novel.
The ‘hells of Beppu’ are a series of brilliantly colored boiling pools that range from blood red to cobalt blue, each with its own character.
Hakodate
Located at the southern tip of Hokkaido, Hakodate has the kind of port-town atmosphere that, in parts, feels more like Europe than Japan, the result of being one of the first Japanese cities to be opened up to foreign trade in the 1850s. The nighttime view of the city from the hillside of Mount Hakodate is said to be one of the best in Japan, and the seafood market in the morning near the waterfront is well worth getting up early for.
Squid is the local specialty, and it comes in forms you might not have considered trying.
Tottori
Tottori is home to something most visitors do not expect to find in Japan: dunes. The Tottori Sand Dunes stretch for nearly 10 miles along the San’in Coast and rise to 165 feet, making them look more like the Sahara than the Japanese countryside.
Beyond the obvious spectacle, the city is also the birthplace of manga artist Shigeru Mizuki, and the nearby Mizuki Shigeru Road is lined with hundreds of bronze yokai monster statues — a surreal and charming tribute.
Matsue
Matsue sits between two large lagoons in Shimane Prefecture and is sometimes called the ‘water city’ for its moated castle and canal-laced streets. The castle itself — Matsue Castle — is one of only twelve original feudal castles still standing in Japan, and on a foggy morning, it looks genuinely imposing.
The city was also home to writer Lafcadio Hearn in the 1890s, whose accounts of Japanese culture introduced the country to Western readers for the first time.
Hikone
Hikone on the shores of Lake Biwa — Japan’s largest freshwater lake — is built around one of the country’s finest surviving castles. Hikone Castle has been standing since 1622 and is designated a National Treasure, putting it in a very short list of structures with that distinction.
The cherry blossoms that bloom around the castle moat each spring are legitimately spectacular, though the town is worth a visit at any time of year.
Sendai
Sendai is the biggest city in the Tohoku region and is a useful entry point for some of northern Honshu’s best scenic spots. Sendai is called the ‘City of Trees’ for its wide boulevards lined with zelkova trees, and the Tanabata Festival, held every August, attracts more than two million visitors for its gigantic paper streamers.
The specialty dish in Sendai is called ‘gyutan,’ or grilled beef tongue, and it is taken very seriously at the many ‘gyutan’ restaurants along Ichibancho Street.
Kagoshima
Kagoshima, at the southernmost tip of Kyushu, lives in the shadow of Sakurajima — an active volcano sitting directly across the bay that periodically dusts the city in a fine grey ash. It sounds unpleasant, but locals have adapted so thoroughly that the whole setup feels oddly normal.
The city has a subtropical climate, excellent black pork cuisine, and strong historical ties to the Satsuma domain, which played a pivotal role in the Meiji Restoration of the 1860s.
Nagasaki
Nagasaki carries a weight that few cities in the world share, but it is also one of Japan’s most layered and culturally rich destinations. For over 200 years, it was the only port open to foreign trade, which gave it a hybrid identity — Chinese temples, Dutch architecture, and Portuguese-influenced cuisine all coexist in a way that feels entirely organic.
The Peace Park and Atomic Bomb Museum are essential and sobering visits, while the hillside Glover Garden offers a different perspective on the city’s outsider history.
Hiraizumi
Hiraizumi in Iwate Prefecture was once the second most powerful city in Japan, a 12th-century cultural capital that rivaled Kyoto in wealth and ambition. Most of it is long gone, but what remains is remarkable — particularly Chuson-ji Temple’s Golden Hall, a glittering structure built in 1124 that survived largely intact and is now a UNESCO World Heritage Site.
The town is small and quiet now, which makes the scale of its past feel even more striking.
Kurashiki
Kurashiki in Okayama Prefecture is best known for its Bikan historical quarter — a canal district lined with white-walled storehouses converted into cafes, craft shops, and museums. The Ohara Museum of Art, housed in a neoclassical building right on the canal, holds an impressive collection of Western art, including works by El Greco, Monet, and Picasso — a genuinely unexpected find in a small Japanese city.
The contrast between the traditional architecture and the European collection is part of what makes Kurashiki memorable.
Toyama
Toyama sits on the coast of the Sea of Japan with the Northern Alps rising directly behind it, creating one of the more dramatic geographical settings of any Japanese city. It is famous for its firefly squid season in spring, when millions of bioluminescent squid light up the bay in an electric blue glow that needs to be seen to be believed.
Toyama is also the starting point for the Tateyama Kurobe Alpine Route, a mountain crossing that passes through walls of snow up to 65 feet high.
Aizuwakamatsu
Aizuwakamatsu in Fukushima Prefecture is one of Japan’s great samurai towns, and it wears that identity with genuine pride rather than as a tourist gimmick. Tsuruga Castle, rebuilt to its original 1592 design, sits at the center of the city surrounded by a wide moat, and the surrounding area is dotted with samurai residences and sake breweries that have been operating for centuries.
The tragic story of the Byakkotai — teenage samurai warriors who died during the Boshin War of 1868 — gives the city a particularly poignant historical layer.
Kotohira
Kotohira on the island of Shikoku is a pilgrimage town built around Konpira-san, one of Japan’s most celebrated Shinto shrines. Reaching the main shrine requires climbing 785 stone steps, and the inner shrine adds another 583 on top of that — making it a genuine physical commitment rather than a casual stroll.
The steep approach is lined with lantern-lit stalls and traditional inns, and the view of the Sanuki Plain from the top is the kind of payoff that makes the climb feel worthwhile.
Japan beyond the obvious
What connects all sixteen of these towns is a sense of place that the big cities, for all their brilliance, can sometimes struggle to offer. Many of them were political, cultural, or economic powerhouses in earlier centuries — places that shaped Japanese history long before Tokyo was even a fishing village.
Visiting them now, you are not just ticking off a list; you are following the actual thread of how this country was built.
The infrastructure has improved enormously in recent years, with the Shinkansen network and regional rail making even remote towns surprisingly accessible, so the old excuse of ‘too hard to get to’ no longer really holds. Japan rewards curiosity, and these towns are proof of that.
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