If you only have 7 full days in Japan, then I would definitely stay in Tokyo. Especially since you’ll be here during the madness that is fall foliage season. If you don’t have accommodation booked already in Kyoto, you’re probably out of luck anyway. Yes, Kyoto has many beautiful temples and shrines, but they’ll be packed to the gills with tourists, both domestic and foreign. Kyoto doesn’t have the monopoly on old temples and shrines, Tokyo and the surrounding area (Nikko and Kamakura to name a few) also have plenty of sites to get your traditional fix in. You could easily spend a week in Tokyo and another week doing day trips, so I wouldn’t worry about not having enough to do there. The next time you come to Japan you could focus on Kyoto and the Kansai area.
For nature, Mt Takao is a really easy day trip from Tokyo - great hiking for all skill levels, the leaves are changing and gorgeous right now, pass through temples on your way up, plus great noodles and beer when you make it to the top of the mountain.
Mt Takao

Thanks for the great help everyone. Because we only have 7 full days we’ve decided to stay in Tokyo and surrounding area.
We’re now planning to do some day trips. Right now we’re thinkkng Hakone, Nikko, and Mt. Takao. Does that sound doable? Is it best to do just two of those? The goal is to get a view of Mt. Fuji and the lakes.
We wanted to stay at a ryokan but it looks like those are more expensive than we had expected (at least in Hakone).

This sounds awesome! Thanks for the recommendation, I had not heard of this location and it looks as though it’ll be beautiful while we’re there.

We’re now planning to do some day trips. Right now we’re thinkkng Hakone, Nikko, and Mt. Takao. Does that sound doable? Is it best to do just two of those? The goal is to get a view of Mt. Fuji and the lakes.
Hakone and Takaosan are easy day trips from Tokyo. Nikko is further and well worth an overnight if you want to see more than the famous shrines/temples. Personally I'd rather do two days Nikko and skip one of the others if all you have is three days.
We wanted to stay at a ryokan but it looks like those are more expensive than we had expected (at least in Hakone).
Ryokan come in all price ranges. Even if you can't afford one of the fancier ryokan, I highly recommend to spend at least one night in a Japanese style tatami room in a cheap ryokan/minshuku which should be available for 4000-5000 yen without or around 8000 yen with food (breakfast/dinner) per person.

Ryokan come in all price ranges. Even if you can't afford one of the fancier ryokan, I highly recommend to spend at least one night in a Japanese style tatami room in a cheap ryokan/minshuku which should be available for 4000-5000 yen without or around 8000 yen with food (breakfast/dinner) per person.
Do you have any recommendations?
It’s funny, now that our trip is only 6 days away my husband is reconsidering splitting time between Tokyo and Kyoto. It would look like this
Day 1 - Tokyo (arrival HND)
Day 2 - Tokyo
Day 3 - day trip Hakone
Day 4 - Tokyo
Day 5 - Kyōto (arrival/travel day)
Day 6 - Kyōto
Day 7 - Kyōto
Day 8 - day trip Nara (?)
Day 9 - Kyōto (travel day back to HND)
Would we need JR pass for this? I’m still thinking likely not but want to be sure.
Is this overly ambitious?
If we stay in Tokyo the entire time it’d be something like this:
Day 1 - Tokyo (arrival HND)
Day 2 - Tokyo
Day 3 - day trip Hakone
Day 4 - Tokyo
Day 5 - day trip ??
Day 6 - Tokyo
Day 7 - Tokyo
Day 8 - Nikko (arrival)
Day 9 - Nikko (travel day back to HND)

It’s funny, now that our trip is only 6 days away my husband is reconsidering splitting time between Tokyo and Kyoto. It would look like this
Day 1 - Tokyo (arrival HND)
Day 2 - Tokyo
Day 3 - day trip Hakone
Day 4 - Tokyo
Day 5 - Kyōto (arrival/travel day)
Day 6 - Kyōto
Day 7 - Kyōto
Day 8 - day trip Nara (?)
Day 9 - Kyōto (travel day back to HND)Would we need JR pass for this? I’m still thinking likely not but want to be sure.
The JR pass would probably turn out slightly more expensive than separate tickets for this, so no. Instead you could get a Hakone Free Pass, which is a good deal if you move around the Hakone area a bit.
Is this overly ambitious?
It is fast, but not impossible. Make sure to travel Tokyo-Kyoto in the (early evening) when sights are closed and the sun has set. This way, you don't lose precious sightseeing time and will have essentially a full day in Kyoto instead of a "travel day".
If we stay in Tokyo the entire time it’d be something like this:
Day 1 - Tokyo (arrival HND)
Day 2 - Tokyo
Day 3 - day trip Hakone
Day 4 - Tokyo
Day 5 - day trip ??
Day 6 - Tokyo
Day 7 - Tokyo
Day 8 - Nikko (arrival)
Day 9 - Nikko (travel day back to HND)
Also possible. What time is your flight out of HND? I'd consider having two full days for Nikko and spend the last day in Tokyo.
If you want another day trip, Kamakura is a popular and good choice and it can be combined with an evening visit to Yokohama on the way back to Tokyo.
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