Japan twin centre holiday: Tokyo and Kyoto, 8 nights

Land in Tokyo and clear immigration, where you will need the Visit Japan Web QR code you registered before flying. The run into Shinjuku takes about an hour by Airport Limousine bus if you land at Haneda, or closer to 90 minutes on the Narita Express if you land at Narita. Private transfers can be arranged in advance.

Your hotel sits in Kabukicho, a few minutes north of Shinjuku station. Once you have dropped your bags, walk ten minutes to Omoide Yokocho, the lane of tiny yakitori counters beside the west exit, or take the free lift to the 45th floor of the Metropolitan Government Building for a first look across the city. Keep the first evening short.

Jet lag wakes you early, so use it. Take the Marunouchi and Ginza lines from Shinjuku to Asakusa, about 35 minutes, and walk in through the Kaminarimon gate while the shutters on Nakamise-dori are still down. The approach to Sensō-ji is a straight 250 metres of souvenir stalls that becomes almost impassable by mid-morning and is empty at seven.

Behind the main hall are the quieter Asakusa Shrine and the five-storey pagoda. When the shops open around ten, work back down Nakamise and into the side lanes for Denbo-in Street and the old craft shops, then cut east to the Sumida River. Rickshaw drivers wait near the gate and will run a ten-minute or half-hour loop of the district.

In the afternoon take the river bus downstream to Hamarikyu Gardens, a walled Edo-period garden with a tea house on an island, or stay on to Odaiba. Either way you arrive by water, with Tokyo Skytree behind you and the city opening out ahead.

An optional pre-bookable full day to Hakone, in the crater country below Mount Fuji. The coach leaves Shinjuku in the morning and covers roughly 90 kilometres south-west, about two hours each way, returning to Shinjuku by 18:00. It has to be booked and paid before you travel; ask us for the current price when you reserve.

The day runs as a circuit: a cruise across Lake Ashi on one of the replica pirate boats, with the red torii of Hakone Shrine standing in the water on the eastern shore, then the Hakone Ropeway up and over the ridge to Ōwakudani. The valley has been venting sulphur since an eruption around 3,000 years ago, and the eggs boiled in the pools come out black; local lore gives you seven extra years of life per egg.

The afternoon is a choice between Gotemba Premium Outlets, one of the largest outlet malls in Japan with Fuji visible behind it, or an onsen with a mountain view. Both work; the onsen is the better use of the day if you have shopping time in Tokyo.

A day on the west side of the city, two stops from Shinjuku on the Yamanote line. Start at Meiji Jingu, where a gravel path runs for ten minutes through forest before the shrine appears, then leave by the south gate straight onto Takeshita-dori in Harajuku. The contrast between the two takes about four minutes on foot and is the point of the morning.

Walk down Omotesando for the architecture, then into Shibuya for the crossing, best watched from the first-floor Starbucks window or from Shibuya Sky. This is also the day for the pre-bookable options: the Harajuku Kawaii tour with a guide in full street style, a kimono and tea ceremony, the Otaku half-day in Akihabara, or a small-group food tour.

The Ghibli Museum at Inokashira Park in Mitaka is 20 minutes west of Shinjuku on the Chuo line. It is small, deliberately unsignposted inside, and holds one short film you cannot see anywhere else.

Check out after breakfast and take the bullet train to Kyoto, 2 hours 15 minutes on a Nozomi service, 476 kilometres at up to 285 km/h. Your tickets are included. Tokaido Shinkansen trains leave from Tokyo station or Shinagawa, so allow 20 minutes on the Chuo line from Shinjuku to Tokyo station plus time to find the platform.

Kyoto station puts you 15 minutes by taxi from Gion, or two stops on the Karasuma subway and a short walk. The city is a grid laid out in the eighth century, which makes it unusually easy to navigate: streets run north to south and east to west, and addresses tell you which crossing you want.

Keep the first evening in Higashiyama. Walk north from your hotel through Gion, along Hanamikoji with its wooden machiya frontages, and up to Yasaka Shrine, lit after dark and open at all hours.

Fushimi Inari is two stops south of Kyoto station on the JR Nara line, about five minutes, and the shrine grounds never close. Thousands of vermilion torii climb the wooded slope of Mount Inari in a tunnel that takes two to three hours to walk in full. Most visitors turn back at the Yotsutsuji viewpoint, halfway up, where the city spreads out below.

Come back down and spend the afternoon in Higashiyama. Kiyomizu-dera stands on a wooden stage over the hillside with no nails in its frame; the descent from it runs through Sannenzaka and Ninenzaka, two stepped lanes of tea shops and pottery, into Kodai-ji and back to Gion.

Photography is banned on the private lanes of Gion after repeated complaints, and the ban is enforced with fines. Walk them, do not shoot them.

Arashiyama sits at the western edge of the city, 20 minutes from Kyoto station on the JR Sagano line. The bamboo grove is a single 500-metre path and it is genuinely quiet only before eight. Beyond it are the villa and gardens of Okochi Sanso, the Togetsukyo bridge over the Katsura river, and the monkey park on the hill opposite, a steep 20-minute climb for a view back over Kyoto.

Tenryu-ji, at the grove's southern entrance, has a garden laid out in the fourteenth century and never redesigned since. The Sagano Romantic Train runs from Torokko Saga up the gorge to Kameoka, 25 minutes each way through the river valley, and pairs with a boat back down the rapids.

In the afternoon cross north to Kinkaku-ji, the gold pavilion on its reflecting pond, then Ryoan-ji and its fifteen stones twenty minutes further west. Bus 11 and the Randen tram both connect Arashiyama to the north-west temples.

Nara was the capital before Kyoto and is 45 minutes south by Kintetsu limited express from Kyoto station, or an hour on the JR Nara line. Kintetsu Nara station leaves you a five-minute walk from the park, which is the better arrival of the two.

The park holds around 1,200 wild sika deer that wander freely between the temples and have learned to bow for food. Tōdai-ji, at the north end, is one of the largest wooden buildings in the world and houses a bronze Buddha cast in 752. Behind it, the stone lanterns of Kasuga Taisha line a forest path uphill, and Nigatsu-do gives you the view back over the whole valley.

If you would rather stay in Kyoto, this is the day for Nishiki Market, the covered food street running five blocks through the centre, the Philosopher's Path between Ginkaku-ji and Nanzen-ji, or the Samurai and Ninja Museum, all bookable through us in advance.

The return flight leaves from Kansai International, built on an artificial island in Osaka Bay. The Haruka limited express runs direct from Kyoto station to the airport in about 80 minutes, roughly every half hour, and is the only rail option that does not involve a change in Osaka. Allow three hours at the airport for an international departure, so a mid-morning flight means leaving Kyoto around dawn.

If your flight is later, most Kyoto hotels will hold luggage after checkout, and Kyoto station itself is worth the last hour: the 15-storey atrium, the rooftop skyway and the ramen floor on level ten. From Kansai you connect through the Gulf and land back at London Heathrow the same day.