Pick two or three bases, not a lap of the country
The fastest way to ruin a honeymoon here is to treat the rail network as a dare. Japan is long, and the trains are so good that an over-full plan looks reasonable on paper and feels like commuting by day four. Two or three bases is the shape that works: a city, somewhere with hot water, and one place that is neither. The shinkansen makes the joins painless, with Tokyo to Kyoto in around 2.5 hours and Kyoto to Osaka in fifteen minutes, so you can move in a morning and still have the afternoon. Book seats together rather than gambling on the non-reserved cars.
Kyoto, taken slowly
Kyoto rewards couples who get up early and then do very little. It was the capital from 794 to 1868, it holds roughly 2,000 temples and shrines, and seventeen of its historic monuments were inscribed as UNESCO World Heritage in 1994, which is exactly why you should not try to see them. Sleep in Higashiyama and the old lanes around Kiyomizu-dera are yours before the buses arrive. Keep Kinkaku-ji for a weekday morning. Arashiyama, on the western edge, is a nationally designated historic site and place of scenic beauty, and its bamboo is best before breakfast. Afternoons are for a garden and a long dinner.
An onsen town, and the rules couples should know
One night in hot water is what people remember, and Hakone is the easy version of it. It is a small spa town in Kanagawa with hot springs in view of Mount Fuji, Lake Ashi and the Hakone Shrine, and it is close enough to Tokyo to be the first or the last stop. Learn the rules before you arrive. You bathe nude, the baths are separated by sex, and mixed bathing is banned in public baths, so a couple who want to share the water reserve a private bath. Wash thoroughly before getting in, keep the small towel out of the water, and check the tattoo policy in advance, because many baths still refuse them.
An island, or a garden city
For the third base, choose water or gardens, and let it be the slow part of the trip. Itsukushima, the island better known as Miyajima, was named one of the Three Views of Japan in 1643 and its shrine is UNESCO World Heritage; a ropeway takes you to within a half-hour walk of Mount Misen at 535 m. Kanazawa keeps Kenroku-en, one of the three great gardens of Japan, laid out as the outer garden of the castle and opened to the public in 1875, and the Hokuriku Shinkansen has reached it from Tokyo in about two and a half hours since March 2015. For sea, the Ryukyu islands are subtropical, and Ishigaki's Kabira Bay sits inside a national park.
A night that is not a hotel: Mount Koya
If you want one night nobody else you know has had, sleep in a temple. Mount Koya is a temple settlement in Wakayama prefecture south of Osaka, the headquarters of the Koyasan school of Shingon Buddhism, with 120 sub-temples, many of which take lodgers as they have taken pilgrims for centuries. UNESCO inscribed Kongobu-ji here in 2004 as part of the Sacred Sites and Pilgrimage Routes in the Kii Mountain Range. The train up takes about an hour and a half by express and around two hours without. Expect early mornings, vegetarian meals and cold corridors, which is the point.
Timing, booking and staying connected
When you go decides how much of the country you share with everyone else. Cherry blossom arrives mid-March into April and the autumn colour from late October to early December, and Kyoto is where the world wants both, so book early and start at dawn. Golden Week in late April and early May, Obon in mid-August and New Year fill trains and hotels, and the rainy season runs early June to mid-July with typhoons from June to December, peaking from July to September. Carry some cash: small restaurants, shrines and rural inns still want it. Nobody expects a tip. Goodbars sells a Japan eSIM you install at home and switch on when you land; it runs on NTT docomo, Japan's largest mobile network by mobile contracts, and our Japan coverage page shows where it reaches and what independent speed tests measure.






