Japan by rail

Best for: Capital cities, traditional culture and crafts, temples, shrines, castles and gardens, historic sites, scenic beauty and nature
Route: Tokyo • Nagano • Kanazawa • Kyoto • Hiroshima and Miyajima • Hakone area (with a Hakone Freepass)
Why do it? To explore Japan’s current and former capitals, be entertained by the snow monkeys and visit a picture-postcard castle. You can also see an o-torii gate that seems to float on the sea and, with luck, Mount Fuji in the Hakone area.

Begin in Tokyo, Japan’s capital since 1868 and a vibrant, crowded city, particularly in the Shinjuku and Shibuya neighbourhoods where skyscrapers and neon lights abound. Yet it also has pockets of peace that offer an escape from the hustle. Take a metro to Meiji-jingu (Meiji shrine) in Harajuku, which is set in a large wooded area and was constructed in honour of Emperor Meiji. On the other side of the city is Kaminarimon, the magnificent entrance gate to Senso-ji, a temple in Asakusa, and leading up to this is Nakamise-dori, a street lined with stalls selling souvenirs and Japanese snacks. Visiting either site offers a good cultural primer, but for an introduction to Japanese history, visit Tokyo National Museum in Ueno. Lastly, before you leave the city, find time to visit its gardens. Hama Rikyu in Shimbashi is an unusual example because the level of its seawater ponds varies with the tides of Tokyo Bay, but Komagome’s Rikugien is the more interesting to visit.

Your next city stop is Nagano, which is known for Zenko-ji, a non-sectarian temple, and is also the jumping-off point for visiting the wild ‘snow monkeys’ in Jigokudani Monkey Park. The best time to see these primates is in winter, as they are more likely to be in their hot-spring baths, but you can watch them grooming each other and playing any time of the year.

For an introduction to the history and culture of Japan, stop at the compact city of Kanazawa. More gold-leaf than anywhere else in the country is produced in this area and it is a great place to learn about Japanese arts and crafts. There’s plenty to see as well. Kenrokuen is deemed one of the three great landscape gardens in Japan, while Myoryu-ji, better known as the Ninja Temple, is an enigma filled with secret tunnels and false doors, so it is not surprising that guided tours are required. The city also has former samurai and geisha districts, a wonderful contemporary art museum and a good indoor food market. And if you’re there at the weekend, grab a shinkansen to Shin-Takaoka, then take the Belle Montagnes et Mer train to Johana to visit Inami, a town known for its wood-carving, or Gokayama where you can see traditional steep-roofed gassho-zukuri houses.

Next up is Kyoto, which was the capital of Japan from 794 to 1868. Unlike many big Japanese cities, it was never bombed, so there remains a lot of historic and cultural interest here. There is more to Kyoto than temples, though. The stunning Nijo-jo (Nijo Castle) and Gion, the geisha district, are both worth a wander, while a short train journey away lies the scenic area of Arashiyama.

However, the city’s most iconic sight remains Kinkaku-ji, better known as the Golden Temple – it even glistens in the rain. And you also can’t leave without seeing Fushimi-Inari (shrine), known for the thousands of torii gates through which you walk when ascending Mount Inari.

As you head west, you can get an impressive view of Himeji Castle for free (even from the shinkansen), but the castle itself is worth seeing up close for its clever design. Further west lies Hiroshima, a city that will forever be known for the devastation caused by the dropping of the world’s first atomic bomb. The museum in Hiroshima Peace Memorial Park includes exhibits such as a mangled tricycle from that day and the testimonies of those who lived through it. It is tough to visit but is a must-see.

For a break from the cities, take a ferry to Miyajima, which is known for the o-torii gate at Itsukushima shrine that appears to be floating on the water. However, don’t leave the island without walking up or taking the ropeway (cable car) to the summit of Mount Misen for views of the islands of the Seto Inland Sea.

On the return journey to Tokyo, take a detour to Hakone, which offers fabulous scenery, especially if Mount Fuji reveals itself. The amazing Hakone Open-Air Art Museum is a good stop, but this is also an onsen (hot spring) area and taking a long soak is a great way to relax after so much travelling around.

Best for: Little-visited towns, nature and scenic beauty, historic temples, an original castle, optional hiking, an onsen town
Route: Narita Town • Sendai for Matsushima • Hiraizumi • Takasaki for Tomioka Silk Mill, Bessho-onsen and Niigata • Matsumoto and Kiso Valley • Kii-Katsuura for Nachi
Why do it? To experience an alternative side of Japan (mostly) away from cities.

Given Narita Town is so close to Narita Airport, one of Tokyo’s main hubs, it is amazing that it remains as unspoilt as it is. Because of this, it makes a great starting point for an offbeat route. Omotesando-dori, the main street, has craft shops and plenty of places preparing eels (the local speciality), and at one end lies the extensive grounds of Naritasan Shinsho-ji temple, which are perfect for exploring after a long flight. For a break, watch the Goma (sacred fire) ceremony.

For your next stop, head north to Sendai for Matsushima Bay, deemed one of the country’s top three scenic spots. Its waters are speckled with over 200 pine-smothered islands, and if you get curious, there are bridges to a couple of them and boat trips leaving from Matsushima that either loop the bay or finish in nearby Shiogama.
Continuing north, stop at Hiraizumi, which was a major centre for culture in northern Japan during the 12th century and has two UNESCO-listed temples. Chuson-ji dates from 850 AD and has temple buildings that spread over a hillside, so expect to do a lot of walking. The other, Motsu-ji, has a ‘Pure Land garden’ that represents Buddhist paradise.

Back towards Tokyo, Takasaki holds little interest in itself but is a great base for a variety of side trips. Bessho-onsen, for example, is a characterful hillside town with plenty of hot springs to relax in, plus some interesting shrines and temples to explore. Here you’ll also find Japan’s only octagonal three-storey pagoda. Fans of sake should also head to coastal Niigata where you can visit a sake brewery, and anyone interested in silk production should grab a train to Joshu-Tomioka for Tomioka Silk Mill, now a UNESCO World Heritage site.

The next stop is Matsumoto, which is set wonderfully against the Japanese Alps. It has an original castle (ie one that has never burnt down) that dates from 1593 and it is also the hometown of iconic Japanese artist Yayoi Kusama. Check out some of her work at the Matsumoto City Museum of Art.

In the days before trains, or indeed any mechanised transport, the only way between Kyoto and Edo (now Tokyo) was on foot or horseback. One such route threaded the Kiso Valley, south of Matsumoto, and was called the Nakasendo (Middle Mountain Way). Rest stops, known as ‘post towns’, dot the way, of which Narai is one of the best-preserved, though Kiso-Fukushima had more significance as it was also a checkpoint. A popular and scenic hiking route is from Tsumago to Magome.

Your final stop lies in the south of the Kansai region. Of all the Kumano shrines in Japan, Kumano Nachi Taisha is the main one and can be accessed from Kii-Katsuura station. The relationship in Japan between Shinto (the state religion until 1945) and Buddhism (which spread here from China) has always been good, and it is not surprising that a Buddhist temple, Seiganto-ji, lies next to the shrine. The view of Nachi waterfall from its pagoda is an iconic image. From the temple, finish with an atmospheric walk on a cedar-tree lined path to the waterfall.

Best for: Seaside and countryside towns with temples and shrines, plus views of Mount Fuji
Route: Take day trips from Tokyo to: Kamakura, Nikko and Kawaguchi-ko
Why do it? A chance to explore more of the Tokyo area.

Kamakura lies 50km south of Tokyo and is a relaxed seaside town that couldn’t be more different to the capital. One of its many highlights is the 13.5m-high Daibutsu (Great Buddha) statue.

The next day, head north to Nikko, which is known for its UNESCO-listed temples and shrines but has some unique sights. The Kanaya Hotel History House is a former samurai house where the 19th-century explorer Isabella Bird once stayed, while Tamozawa Imperial Villa Park was once a royal holiday home but is now open to everyone.

Lastly, the journey to Kawaguchi-ko, particularly from Otsuki, can be very scenic in the right weather. It is also the only place where you can see a reflection of Mount Fuji in a lake.

Best for: A laid-back city, an old onsen town, sand
dunes and sculptures, an award-winning garden
Route: Osaka • Kinosaki-onsen • Tottori • Yasugi
Why do it? For anyone flying into Kansai International Airport and wanting varied experiences.

Osaka is Japan’s second city and a commercial hub, but it also has some kitsch areas and relaxed vibes. To get an idea of how much it has changed, pay a visit to the Shin-Sekai area, which recalls how downtown Osaka looked in the 1950s/60s. Elsewhere, the neon lights of Dotombori (Namba station) bring you back to the present, while Abeno Harukas, near Tennoji station, offers citywide views from the tallest building in Japan (though it is due to lose that title to a building in Tokyo in 2023).

For a slower pace of life, take a train north to Kinosaki-onsen, a charming old hot-spring town set on a willow-lined river. It is accepted in onsen towns that you can walk around in a yukata (a light kimono). You can also visit any, or all, of the seven public baths, which are free to anyone staying in a ryokan (inn) in town.

Some 80km to the west of Kinosaki-onsen, you’ll find the largest area of sand dunes in Japan at Tottori. It is an unexpected sight, and nearby is even a sand museum where the theme for its huge, detailed sand sculptures changes annually. It is best visited between April and December as the artists are at work creating their masterpieces in late winter.

Continue west for your final stop: the Adachi Museum of Art in Yasugi. Its name gives little idea that this is actually a garden interspersed with a contemporary art gallery. It can be frustrating that you can only observe the garden from a distance (as you would a painting), rather than walk around it, but viewing a garden as a work of art gives food for thought.

Best for: Edo-period gardens, visiting an art island, kabuki theatre, rural scenery, ancient hot-spring towns
Route: Takamatsu and Naoshima • Kochi • Dogo-onsen • Kan-onji
Why do it? To really get off the beaten track.

Begin by taking a train over the Seto-Ohashi Bridge from Okayama to Takamatsu. When you arrive, be sure to visit Ritsurin-koen, an expansive landscape garden, then stroll around the amazing art island of Naoshima, which is accessible by ferry.

Your next stop is Kotohira, which has a wonderful hilltop shrine and the oldest wooden kabuki theatre in Japan (there is also a good one at Uchiko). For scenic gorge walks, head south for Oboke, then continue on to the historic streets of Kochi, whose castle retains its original Edo-period architecture.

In the west of the island, Dogo-onsen, near Matsuyama, has a 3,000-year-old history and is an atmospheric place to visit, even if it is being renovated. And as you head back to Takamatsu, stop at Kan-onji for the Zenigata suna-e, a massive coin-shaped sand carving that dates back to 1633.