Days 1–3 — Tokyo
Land at Narita or Haneda and get a 7-day Japan Rail Pass sorted before you leave the airport if you plan to use it (it must be activated within 3 months of a foreign passport entry stamp, though as of recent years it can also be bought inside Japan at a markup). Buy a Suica or Pasmo IC card immediately — it covers virtually every train, subway, bus, and convenience-store purchase for the whole trip.
Day 1: ease in with Shinjuku and Shibuya. Shibuya Crossing, Shibuya Sky at sunset, then Omoide Yokocho for yakitori and beer in one of the tiny alleyway bars. Day 2: old Tokyo — Senso-ji and Asakusa in the morning (go early, before the tour groups), Ueno Park and a museum if you want art or history, then Akihabara in the afternoon for the electronics-and-anime district. Day 3: Meiji Shrine and Harajuku's Takeshita Street in the morning, Omotesando for design and lunch, teamLab Planets or Borderless in the afternoon if you booked ahead (tickets sell out), and Tokyo Skytree or Shibuya Sky again at night if you want a second skyline view from a different angle.
Base yourself in Shinjuku or Shibuya for the best rail connections. Three days is enough to get a real feel for Tokyo without exhausting yourself before the rest of the trip.
Day 4 — Hakone
Take the Odakyu Romancecar or a JR route to Odawara, then transfer onto the Hakone Tozan railway. Buy the Hakone Free Pass at Shinjuku station — it covers the local trains, cable car, ropeway, and pirate-style sightseeing boat on Lake Ashi in one ticket.
Spend the day on the Hakone loop: the switchback mountain railway to Gora, the cable car up to Sounzan, the Hakone Ropeway over the volcanic Owakudani valley (black eggs boiled in the sulphur springs are the local snack — eating one supposedly adds seven years to your life), then down to Lake Ashi for the boat crossing. On a clear day, Mount Fuji is visible across the lake — this is one of the most reliable easy viewpoints in the region.
Stay one night in a ryokan with an onsen (hot spring bath) if your budget allows — it's the single best way to experience traditional Japanese hospitality, and Hakone has more options at accessible price points than Kyoto or Tokyo. Otherwise, a late-afternoon return to Tokyo or a direct connection toward Kyoto is possible via Odawara's Shinkansen stop.
Days 5–7 — Kyoto
Take the Shinkansen from Odawara or Tokyo to Kyoto (roughly 2 hours from Tokyo). Three days here covers the essentials without rushing.
Day 5: Fushimi Inari Taisha first thing — arrive by 7am to walk the tunnel of thousands of red torii gates before the crowds build, then head into central Kyoto for Nishiki Market and lunch. Day 6: Arashiyama in the morning for the bamboo grove and Tenryu-ji temple, then back into the city for Kinkaku-ji (the Golden Pavilion) in the early afternoon before the light changes. Day 7: Higashiyama district — Kiyomizudera temple, the preserved streets of Sannenzaka and Ninenzaka, and Gion in the early evening for a chance of spotting a geiko or maiko heading to an appointment.
Stay in or near Gion or Kawaramachi for atmosphere and walkability. If your flight home departs from Tokyo, factor in a final Shinkansen back (2 hours) or fly out of Kansai International near Osaka, 90 minutes from Kyoto, if your itinerary allows it — often the more efficient way to close a one-week loop.