Okay so when I started planning three weeks in Japan as part of a much longer sabbatical, I made one rule for myself: no backtracking. What I ended up with was basically a loop. You start loud, in Tokyo, and you end up on a literal mountain with monks. In between there’s a lakeside art museum, two totally different onsen towns, a city almost nobody talks about (their loss), the temple-packed streets of Kyoto, the food chaos of Osaka, and then a night sleeping inside an actual working Buddhist temple.
Here’s the whole route, stop by stop, with the pacing and transit stuff that made it actually work. Plus what I’d tell a friend before they book anything.
The Shape of the Trip
Tokyo (7 nights) → Hakone (2 nights) → Shima Onsen (2 nights) → Kusatsu Onsen (2 nights) → Kanazawa (5 nights) → Kyoto (5 nights) → Osaka (4 nights) → Koyasan (2 nights)
That’s about three weeks and yes, it’s front loaded on purpose. Tokyo gets a full week because there is simply too much city to see in less time, and also because after a 12+ hour flight you deserve to ease in instead of sprinting from day one like a maniac. Every stop after that gets a little shorter and a lot quieter. By the time you’re in Koyasan you’ve gone from six lane pedestrian crossings to a single dirt path through a cedar forest with 200,000 gravestones. Wild range for one trip.
Tokyo: Give It the Whole Week, I Mean It
I stayed at CITAN Hostel in Nihonbashi and honestly it was a great call. Central, easy to get around from, close to both the old school neighborhoods and the busier west side of the city.
Here’s the thing with Tokyo. Don’t treat it like a checklist. Let the neighborhoods have their own days instead of trying to cram everything into one manic itinerary.
- Asakusa, obviously. Sensō-ji, Nakamise Shopping Street, and if you’re into cookware, Kappabashi’s kitchen supply stores will ruin you. There’s a knife shop there called KAMATA Hakensha that I still think about more than is normal.
- Yanaka, my personal favorite. This is the most “old Tokyo” neighborhood left, mostly because it dodged wartime bombing. Do the temple walk, get lost in Yanaka Ginza, and don’t overthink it. This is a neighborhood built for wandering with no plan.
- Shinjuku. Do Omoide Yokocho and Golden Gai at night, then Shinjuku Gyoen during the day for a total mood reset. Also there’s a hidden torii tunnel at Hanazono Shrine that nobody tells you about.
- Shibuya and Harajuku. Yes the crossing is worth the hype, I said what I said. Pair it with Miyashita Park’s rooftop and the walk down Cat Street into Harajuku, it softens the chaos a bit.
One thing to plan for way ahead of time: Toyosu Market’s tuna auction viewing is a lottery, not a walk up situation. I applied the second I had my dates locked and got a 5:30am slot. If tuna auctions are even slightly your thing, apply immediately, it fills up fast.
Transit tip: get an IC card (Suica or Pasmo) at the airport the second you land. You will use this thing for trains, buses, and even vending machines for your whole trip. Non negotiable.
Hakone: It’s a Loop, Not a Checklist
From Tokyo, the Romancecar runs straight from Shinjuku Station to Hakone Yumoto in about 90 minutes. No transfers, reserved seats, genuinely relaxing. This is where the Hakone Freepass earns its keep, one pass covers the trains, buses, ropeway, and cable car you’ll be using for the classic Hakone loop.
Two nights works if you’re efficient about it, but only if you accept you won’t see it all. I prioritized:
- The Hakone Open Air Museum. The Picasso Pavilion alone is worth the ticket. I skipped the Okada Museum of Art but they’re on the same bus route if you have the time.
- The Owakudani ropeway for the volcanic valley views, then straight into the Hakone Tozan Cable Car back down to Gora.
- Hakone Shrine at Motohakone. Fair warning, the famous floating torii gate was closed for maintenance when I went, and that photo is basically the whole reason people come, so check ahead.
If you only have time for one onsen dip in Hakone itself, day use spots like Tenzan Onsen or Hakone Yuryo let you soak without committing to a full ryokan stay.
Pacing note: don’t think of Hakone as stops on a list, think of it as a loop you move through. Build your day around the ropeway and cable car network, not around museum hours.
The Onsen Towns: Shima Onsen and Kusatsu
This part of the trip is the one I’d tell people not to skip, because it’s the part most people don’t even know exists. After the polish of Hakone, Shima Onsen and Kusatsu Onsen are a hard reset. Rural, quiet, and mostly Japanese speaking only.
Shima Onsen (2 nights) is barely even a town, more like a handful of ryokan scattered along a river gorge. You can hop between public bathhouses like Kami no yu and Kawara no yu. There’s no real “sightseeing” beyond the Lake Okushima observation deck and a quick walk to Momotaro Waterfall. Honestly that’s the whole point.
Kusatsu Onsen (2 nights) is livelier and way more famous, thanks to Yubatake, the “hot water field” that’s basically the town’s whole personality. Try to time your visit around a yumomi performance, where locals cool the scalding spring water with giant wooden paddles set to a folk song. It’s touristy in the best possible way, a genuinely old tradition that also happens to be a great show.
Real talk on transit here, this is the least convenient stretch of the trip. Getting between Hakone, Shima Onsen, and Kusatsu means a mix of local trains and buses with real gaps in the schedule. Budget more time than Google Maps tells you, and do not book anything tight on either end of a travel day. Learn from my mild panic.
Kanazawa: The City Everyone Skips and Shouldn’t
Five nights in Kanazawa was the decision I was least sure about before the trip and the most sure about after. It’s smaller than Tokyo, Osaka, or Kyoto, and it doesn’t get nearly the same hype, which is honestly exactly why you should go.
I based myself centrally at Tokyu Stay Kanazawa and used the bus loop that connects basically everything worth seeing. Higashi Chaya District, Kenroku en (one of Japan’s three great gardens, and it earns it), Kanazawa Castle Park, Nagamachi Samurai District, Omicho Market, and the 21st Century Museum of Contemporary Art. The bus takes IC cards, and if you’re doing more than four or five rides, just get the day pass at the station.
But honestly what made Kanazawa stick with me was the hands on stuff, not the sightseeing:
- A gold leaf pasting workshop at Hakuichi. Yes, gold leaf ice cream is a real thing. Yes, get it.
- A pottery wheel workshop at Kutani Kosen Kiln.
- A ring making class.
- Just wandering the teahouses in Higashi Chaya with zero agenda.
If you only have time for one craft experience, make it the gold leaf. It’s Kanazawa’s whole thing, it shows up in everything from lacquerware to dessert.
Kyoto: Five Days and Still Not Enough
Kyoto is the center of gravity for this whole trip, and five nights felt like the bare minimum without rushing. The move here is grouping temples by area. Kyoto’s sights sprawl all over the city, and zigzagging between neighborhoods will eat your whole day in trains.
Roughly how I split it:
- Day 1, south and east: Fushimi Inari Taisha early to beat the crowds through the Senbon Torii, then Tōfuku ji and Sanjūsangendō, ending at Kiyomizu dera and the Sannenzaka and Chawanzaka lanes at golden hour.
- Day 2, Arashiyama: the bamboo grove is famous for a reason but pair it with the quieter Okochi Sanso Garden and Jōjakkōji Temple, then get to Tenryu ji before the crowds show up.
- Day 3, Higashiyama and Philosopher’s Path: Ginkaku ji, the actual Philosopher’s Path, Eikandō, and Nanzen ji. This was the calmest, most unhurried day of the whole trip.
- Day 4, Gion and northwest: Gion in the late afternoon for the atmosphere, and if you have energy, Kinkaku ji and Ryōan ji’s rock garden earlier in the day.
- Day 5: buffer day, no plan required. I used mine for the Kurama to Kibune hike, a genuinely peaceful little escape through forested hills dotted with shrines. Also totally acceptable to just redo whatever you rushed.
Quick heads up, a lot of Kyoto’s best temples have specific closing days, often Wednesdays or Mondays. Double check before you build a whole day around one, learned that one the annoying way.
Osaka: The Food Detour
Four nights in Osaka is really a decompression stop after Kyoto’s temple overload, and mostly an excuse to eat nonstop. Osaka Castle and Shitennō ji are each worth a morning, but the real itinerary here is Dotonbori, Kuromon Market, and Shinsekai, ideally with an actual food tour so you have context instead of just wandering and pointing at menus like an idiot (I did one starting at DAIICHI本店, would recommend).
If you’re traveling with anyone who needs a full theme park day, Universal Studios Japan is right there too, easy half day or full day depending on your line tolerance.
Transit note: Osaka is the last big hub before things get quiet, so use it to restock, do laundry, and handle logistics before Koyasan, where amenities basically disappear.
Koyasan: Ending on a Mountain
Two nights here closes the whole loop, and honestly I don’t think this itinerary works without it. Koyasan Special Head Temple Shojoshin in is a real, functioning Buddhist temple that takes overnight guests. You sleep on tatami, eat shojin ryori (Buddhist vegetarian cuisine), and can join the morning prayer service if a 6am start sounds appealing to you, which, no judgment either way.
The big pilgrimage here is Okunoin Cemetery, over 200,000 gravestones under towering cedar trees, ending at Kobo Daishi’s mausoleum. Walk it at dusk if you can swing it. The lantern lit path at Torodo, the Lantern Hall, is a completely different experience than seeing it in daylight.
Getting up here from Osaka takes a cable car and a short bus ride up the mountain, and honestly that ride is one of the few times on this trip where the journey itself felt like part of the destination.
Pacing Lessons, Looking Back
A few things I’d tell anyone building their own version of this route:
- Put your energy into Tokyo, not your itinerary. A full week means you get to actually absorb it instead of racing through it. Save the “must see everything” panic for the shorter stops later.
- The onsen towns are the hardest to reach and the easiest to cut. Don’t cut them. They’re the clearest contrast to literally everywhere else on this trip.
- Kanazawa is not a detour, it’s a highlight. If you’re tight on time, cut a day from Tokyo before you touch Kanazawa.
- Buy the regional passes before you actually need them. The Hakone Freepass and the Kyoto and Osaka bus day passes pay for themselves within a handful of rides.
- Build in at least one true buffer day. Mine was in Kyoto and ended up being one of my favorite days of the whole trip, precisely because it had zero plan attached to it.
Three weeks sounds like a lot until you’re standing in Tokyo realizing you’ve barely scratched Asakusa. This route won’t let you see everything, nothing will, but it moves through Japan in a way that actually makes sense on the ground. City to mountain to onsen to temple, without ever doubling back.