The best two-week Japan itinerary is the one with the fewest hotel changes. Three bases, two long train journeys, and enough slack that a rainy day doesn't destroy the plan.
Days 1–5: Tokyo
Land, get an IC card, and do not schedule anything demanding on day one. Then:
- Day 2 — East side: Asakusa early, the Sumida river, Kiyosumi Garden, dinner in Kuramae.
- Day 3 — Old Tokyo: Yanaka and Nezu on foot, Ueno museums, Jimbōchō book district.
- Day 4 — West side: Shimokitazawa in the morning, Shibuya and Ebisu at dusk.
- Day 5 — Day trip to Kamakura or Nikkō.
Days 6–7: The interlude
Pick one, depending on season and taste:
- Hakone — onsen, an open-air museum and Fuji views if the weather cooperates.
- Kanazawa — gold leaf, one of Japan's three great gardens, a preserved samurai district and superb seafood.
- Kinosaki Onsen — a hot spring town where guests walk between seven public baths in yukata.
Send your suitcase ahead to Kyoto by courier and travel with an overnight bag.
Days 8–11: Kyoto
Follow the four-day Kyoto itinerary — Higashiyama, the northern gardens, Arashiyama, Fushimi and Uji, each timed around the quiet hours.
Day 12: Nara or Osaka
Nara for the Great Buddha, the deer park and Isuien garden; Osaka for Dōtonbori, the kitchen district and a completely different civic personality — louder, funnier, more direct.
Days 13–14: Back to Tokyo
Return by Shinkansen, spend the last full day on whatever you missed, and stay near the airport line for an early flight.
What this itinerary deliberately leaves out
Hiroshima, Kōya-san, Hokkaido and Kyushu. All are excellent, and all turn a fortnight into a series of transfers. Japan is easy to return to; a first trip is better spent going deeper than wider.
For costs, see two weeks in Japan on a real budget. For timing, the best time to visit Japan.