The 16 best underrated destinations in Japan

Sendai has long been one of Japan’s great unsung destinations, but we’re onto that – it’s in our two-week itinerary, after all. But Matsushima, just 20 minutes by train from Sendai, is worth a visit in its own right. Matsushima Bay’s 260-odd islands were named one of the ‘Three Views of Japan’ back in the 1600s – they’re still just as gorgeous today. Our advice? Get there at sunrise to see the islands sharpen into focus with the light, then spend a morning trekking around Oshima and Fukuura islands (crossing the legendarily lengthy Fukuurabashi footbridge), before getting a cruise in the afternoon. Or spread it all out, savouring each bit of the islands, their temples and beaches (as well as Matsushima’s accompanying resort town) over another day or two.

Squeezed on two sides by the ocean, much of the northern city of Hakodate sits hunkered down from the cold, its buildings better resembling those of Iceland or Alaska than the rest of Japan. But this is a fabulously well-rounded city. Hakodate’s long history of foreign trade and influence has left fascinating marks on its local architecture (like the churches of Motomachi or the blustery, solitary Foreigners’ Cemetery). Not forgetting, of course, Mount Hakodate, widely remarked as one of Japan’s great night views. Get to the top well before sunset, walk around a bit (be sure to look out south, too), then get yourself a good spot to see how the city lights shimmer from above between two inkily dark swathes of ocean. Shin-Hakodate is also handily linked to Tokyo by a direct (albeit long, five-hour-plus) shinkansen.

Toyama is known as a great base from which to explore the western side of the Japanese Alps, offering easy access to Takayama, Tateyama, Shirakawa-go and Gokayama. And while it certainly is a solid base for those trips, the city itself often gets overlooked. From its awesome glass museum to its curiously empty stretches of beach, most unmissable is Amaharashi: a lone rock out in the middle of the sea with a singular tree on it, mighty snow-capped peaks soar in the background. I’d suggest staying out near Iwase on the coast – being so close to the beach is priceless, plus the tram to the centre of Toyama runs late into the night.

Whilst a massively popular destination for domestic and Asian travellers, Fukuoka is often simply too far from Tokyo and Osaka for most first-time visitors to Japan. But it’s absolutely worth the trek. A not-too-bad five-hour train from Tokyo (to Hakata), you’ll be greeted by a sunnier climate, laid-back vibes and a food scene that, even by Japanese standards, is a cut above. Home of tonkotsu ramen chain Ichiran and known for its buzzy yatai street food stalls, Fukuoka is such a rampant foodie city that you’ll struggle not to eat exquisite nosh at every turn. Don’t miss out on its party culture, either: there are few better ways to follow-up some grub at a yatai than with drinks and live music on one of the city’s bridges.

Shizuoka prefecture is primely positioned for two of Japan’s most revered culinary assets. Home to Japan’s biggest and deepest fishing ports, it’s a fish-lover’s heaven, but the wider prefecture is also known for its green tea – 40 percent of the country’s tea is grown here. All of which makes Shizuoka city one of the finest places in the country to tuck into some fresh fish and sip some green stuff. But that isn’t all. Also home to the burial place of legendary shogun Tokugawa Ieyasu, climb (or get the cable car) over 1,000 steps up Mount Kunozan and take in endless views of the Pacific, before rambling down and walking the coastal road north to Miho no Matsubara, a beachside pine forest and one of the finest spots to view Mount Fuji in all its conical might.

Sand dunes? In Japan? You bet. Nine miles long and about a mile-and-a-half wide, Tottori’s white, pristine sand dunes stretch all the way into the city centre and make it seem more Saharan than Japanese – and they’re a major part of the city’s appeal. There’s even camels and an entire museum here dedicated to sand sculptures (The Sand Museum), which is the world’s only permanent sand art space. Done with the sand? Don’t fear. Tottori has plenty more to see and do, much of which focuses on sites of natural beauty like Mt Daisen (and its temple, Daisenji), the rugged Uradome coastline and the vast Hanakairo flower park.  

There’s so much more to Kobe than wagyu and its infamous 1995 earthquake – though both, as you can imagine, have come to define this city on the Seto Inland Sea. Squeezed between mountains and sea, there’s something in Kobe for everyone. From museums dedicated to traditional woodcraft and architectural maestro Tadao Ando to vast flower gardens, winding waterfall trails and one of Japan’s most bustling Chinatowns, the marina has a peaceful, spacious Mediterranean sort of feel. Add to all that the thriving music scene, marvellous shopping and diverse food offerings of Sannomiya, Kobe’s charms are endless.

Japan’s largest freshwater lake, the Biwa-ko (or ‘Lake Biwa’) is just 15 minutes’ train north of Kyoto. About 64 kilometres long, it gets its name for looking a little like a ‘biwa’ – a traditional Japanese instrument that’s a bit like a guitar – and it’s been a centre of trade and commerce for centuries. These days the Biwa-ko is best known for recreation: plenty of water-sports and other events take place on the lake and its surrounding beaches. Spend a few days getting trains around the lake, taking in its scenic beauty and stopping off at places like Hieizan Sakamoto (where you can get a cable car up to Mount Hiei, one of the most important spots in Japanese Buddhism), Omi Hachiman (known for its traditional canals), Hikone (and its preserved castle), Omi Takashima (with its floating torii gate), Omi Maiko (for its beaches) and Otsu (the buzzing capital of Shiga prefecture).

The home of Sapporo beer (obvs), a mesmerising annual Snow Festival and more winter sports than you ever knew existed, Sapporo is the biggest city on Hokkaido and the island’s cultural, economic and political powerhouse. Not yet linked by Shinkansen (that’s all set for 2030), it’s easily reached by internal flight. Most of all, however, it’s a fab city to really get to grips with Hokkaido’s regional identity, from its history and food to its parks and architecture. Be sure to check out the Sapporo Clock Tower (the oldest of its kind in Japan) for an endearingly thorough – and totally free – tour detailing the history of the building. Oh, and make sure to visit in the snow heights of winter. That’s when this city really comes into its own.

A three-hour flight from Tokyo, the islands of Okinawa are far closer to Taiwan than Japan and boast a totally different climate, namely that of a tropical island. The culture of the local Ryukyu people is distinctly different from the rest of Japan, too – and Naha, the biggest city in Okinawa, is a great place to get to grips with it all. Be sure to check out Okinawa’s different styles of temples, shrines and castles (especially Shuri Castle), as well as try out some Okinawan specialities like Orion beer and Blue Seal ice cream. The sweeping, pristine tropical beaches should be the main priority here – they’re the reason most domestic travellers love heading down to Okinawa for a beach vacay.

The ‘Naples of Japan’ sits, just like its Italian counterpart, in the ashy shadow of a massive smoking mount. Japan’s most active volcano Sakurajima lies just across the bay from Kagoshima – but, much like Vesuvius, it’s totally safe to visit. Getting a short ferry across the bay and hiking through the lush volcanic vegetation is one of visitors’ most popular things to do. Kagoshima itself is renowned for its hot, dry climate and palm tree-lined streets, as well as for being a base for trips out to hiking spot Yakushima island. You won’t find a better spot to take in a full view of Sakurajima billowing smoke over the city than Shiroyama Park, with bustling Kagoshima in the foreground and the ash-belching giant in the distance.

Likely known outside Japan as the second target of the US atom bomb campaigns in the Second World War, it’s difficult to emphasise just how much more there is to Nagasaki than its atomic victimhood (though the Peace Park, Peace Memorial Hall and Atomic Bomb Museum are just as harrowing, informative and persuasive as their equivalents in Hiroshima). A harbour city sprawled between dense, green valleys, Nagasaki has lots of small, winding streets across steep hills. As the site that foreign missionaries first settled in Japan, it’s also got plenty of non-atom-bomb history, as well as an energetic, fabulously gaudy entertainment district and, in Mount Inasa, another of Japan’s most spectacular night-time views. On top of all that, Nagasaki is also the access point for trips to the abandoned island of Gunkanjima and boasts the country’s newest (and most swish) bullet train route.

There’s so much to cram into Tokyo and its most popular day trips (Kamakura, Takao and so on) that few international visitors manage a visit to Yokohama, which is Japan’s second-largest city and within very, very easy reach of the capital. More than just an industrial powerhouse, Yokohama is home to the largest of Japan’s Chinatowns (the others being in Kobe and Nagasaki), a sprawling waterfront, the world’s biggest clock (which is also a Ferris wheel, Cosmo Clock 21) and not one but two museums all about ramen. Both the Cupnoodles Museum (which is about instant ramen) and the Ramen Museum (about the classic stuff and all its varieties) are musts for lovers of slurpy noodles ‘n’ soup.

By Wakayama, we’re talking about the prefecture and not just its capital city. This place is all about its natural beauty, much of which revolves around the ancient Kumano Kodo pilgrimage routes which sprawl across the Kii Peninsula. Whether you attempt the route in one go (taking approx four-and-a-half days) or do small sections, expect to stumble across temples, shrines, onsens, ryokans, waterfalls and viewpoints. And Wakayama’s charms extend far beyond the Kumano Kodo: there’s also a huge range of adventure activities throughout the prefecture, from kayaking to caving, plus it boasts some of the clearest, least polluted (and so best stargazing) skies in all of Japan.

Despite being the smallest of Japan’s four main islands, Shikoku is still huge – and much of it has nowhere near the same amount of traveller-friendly infrastructure as Japan’s more popular tourist spots. The island’s features range massively, from some of Japan’s most industrialised areas to its most unspoiled and isolated areas of natural beauty like mountains and beaches. The port city of Takamatsu is a key entry point for those wanting to explore Shikoku’s interior, ideal for launching into national parks and the island’s 88-site traditional pilgrimage. But Takamatsu itself shouldn’t be ignored. Don’t miss the castle – known for its seawater moats – nor the Ritsurin-koen, one of the most immaculately-kept traditional gardens in the country.

Sitting two-and-a-half hours’ ferry from Niigata (which itself sits a couple of hours northwest of Tokyo by Shinkansen), the island of Sado offers spectacular natural sights, carefully preserved culture and fascinating history in spades. Japan’s sixth-largest island was historically a place of exile for prominent political outcasts, though it’s also known for its gold mines (Sado kinzan), the five interlinked bays of Senkakuwan and for being wedged between two mountain ranges. While much of Japan is primed for a road trip, that’s especially the case with Sado. There are few better ways to take in the entirety of this island than routes such as the Osado Skyline, which rises up 900 metres from sea level and features views of everything from mountains and plains to forests.