The single most common routing mistake on Japan itineraries is backtracking. You fly into Tokyo, take the Shinkansen to Kyoto, move to Osaka, then ride 2.5 hours back to Tokyo to catch your flight home. That return trip costs a full travel day and ¥14,000+ in Shinkansen fares, and the only thing you see on that day is the inside of a train. Almost everything about route planning comes down to avoiding this: go in one direction, use fewer bases, and stop treating the map like a menu where you jump between whatever sounds good.
Which direction should you go?
Japan's main Shinkansen line runs in a straight line: Tokyo, Nagoya, Kyoto, Osaka. If you're visiting those cities, you should move in one direction along that line. The direction depends on which airports work for your flight.
Tokyo first, Kansai last works if you can fly into Narita or Haneda and out of Kansai International (KIX). Start in Tokyo, work your way through any stops between (Hakone, Nagoya, the Alps), and end in the Kyoto/Osaka area. Your last day is a short train from Osaka to KIX, not a 3-hour backtrack to Tokyo.
Kansai first, Tokyo last works if you fly into KIX and out of Narita or Haneda. Same idea in reverse. Land in Osaka, do Kansai, move northeast. You end in Tokyo near your departure airport.
Either direction is fine. What matters is that you don't bounce back. If your cheapest flights are round-trip into Tokyo, the route becomes Tokyo → Kansai → Tokyo, and that last Shinkansen is unavoidable. But even then, you save time by doing all your Tokyo sightseeing at the beginning, moving west in one shot, and keeping only the final transfer day for the return.
Do you need to fly back to where you started?
No. An open-jaw ticket (fly into one city, out of another) often costs the same as a round-trip or close to it. That premium pays for itself immediately: you skip a ¥14,000 Shinkansen return and save an entire travel day. Search for multi-city flights on Google Flights or Skyscanner. Tokyo (NRT/HND) to Osaka (KIX) or vice versa is the most common open-jaw pairing for Japan.
If open-jaw pricing doesn't work for your route, the next best option is a domestic flight. Peach and Jetstar Japan run cheap flights between major cities (Osaka to Sapporo, Fukuoka to Tokyo) starting around ¥4,000-8,000 one way, which is often less than the equivalent Shinkansen ticket and takes half the time.
How many cities can you fit?
Fewer than you think. Every city change costs half a day in checkout, luggage logistics, transit, and waiting for check-in (3pm at most Japanese hotels). Here's what works at each trip length:
| Trip length | Cities | Hotel changes | Example split |
|---|---|---|---|
| 7 days | 2 | 1 | Tokyo 4 nights + Kyoto/Osaka 3 nights |
| 10 days | 2-3 | 1-2 | Tokyo 4 + Kyoto 3 + Osaka 3 |
| 14 days | 3-4 | 2-3 | Tokyo 5 + Hakone 1 + Kyoto 4 + Osaka 3 + fly from KIX |
| 21 days | 4-5 | 3-4 | Tokyo 5 + Alps 3 + Kyoto 4 + Hiroshima 3 + Fukuoka 3 + fly from FUK |
The number that matters isn't cities visited, it's hotel changes. Each one burns time. If you can cover an area with day trips from a single base instead of moving hotels, you'll see more and spend less time packing.
The two bases that cover almost everything
Tokyo and Osaka are hubs for a reason. From Tokyo, you can day-trip to Kamakura, Nikko, Hakone, Kawaguchiko, and a dozen other places without changing hotels. From Osaka, Kyoto is 15 minutes by Shinkansen, Nara is 35 minutes by Kintetsu express, Kobe is 20 minutes by JR, and Himeji is 30 minutes by Shinkansen or about an hour on the regular JR rapid. A 10-day trip split between these two bases, with day trips from each, covers the Golden Route and more without the constant hotel shuffling.
Kyoto works as a Kansai base too. The trade-off: cheaper food and nightlife in Osaka, better temple access in Kyoto. If your main Kansai activities are temples and shrines, Kyoto is the better base. If you want the food scene and a more energetic neighborhood at night, Osaka is the pick.
Three routes that work
The Golden Route (7-10 days)
Tokyo → Kyoto → Osaka. The Shinkansen connects all three in a straight line, so you move in one direction the whole trip. 4-5 nights in Tokyo with day trips, then move to Kansai for the rest. Fly out of KIX to avoid the return trip. This is the first-timer default because it works.
The Extended Loop (14 days)
Tokyo → Hakone (1 night) → Kyoto (3-4 nights) → Osaka (2-3 nights) → Hiroshima (2 nights, with Miyajima as a day trip) → fly from Osaka or Hiroshima. This adds western Japan without doubling back. The Shinkansen from Osaka to Hiroshima is about 90 minutes, so the extension is easy. Going beyond the Golden Route doesn't mean going further. It means going deeper into fewer places.
The Alps Route (14-21 days)
Tokyo → Kanazawa (2-3 nights, with Takayama and Shirakawa-go) → Kyoto → Osaka. This adds the Japanese Alps between Tokyo and Kansai. The catch: there's no direct Shinkansen between Kanazawa and Takayama. You take the Shinkansen to Toyama (20 minutes) then transfer to the Limited Express Hida to Takayama (about 90 minutes). Around 2 hours total with the connection. Worth it if you want mountain towns and traditional villages between the big cities.
What about Hokkaido and Okinawa?
Both are separate trips within your trip. Hokkaido is far enough north that flying from Tokyo to Sapporo (90 minutes, ¥5,000-15,000 on budget airlines) makes more sense than the 8-hour Shinkansen. Okinawa is a flight from anywhere on the main island (2-3 hours from Tokyo, 2 hours from Osaka). Bolt either onto the start or end of your route, not the middle. If you wedge Sapporo between Tokyo and Kyoto, you're flying north and then flying back south, which is the airborne version of Shinkansen backtracking.
The real routing test
Draw your route on a map. If the line crosses itself, you're backtracking somewhere. Every crossing is a half-day or more of travel that could be eliminated by reordering your stops. The most common crossings: returning to Tokyo from Kansai just to fly home, bouncing between Tokyo and a day trip destination with a hotel change in between, and doing Hiroshima before Kyoto when you're coming from Tokyo (Kyoto is on the way, Hiroshima is past it).
Your hotel location matters here too. If you're based in Shinjuku for your Tokyo days, your departure station is Shinjuku for day trips west (Hakone, Kawaguchiko) and Tokyo Station for the Shinkansen south. Picking a hotel near the station you'll use most saves 20-30 minutes per trip.
The free itinerary checker maps your route and flags every backtrack. Paste your itinerary in any format, and it shows you where you're crossing your own path and how to fix the order.