24 days in Japan itinerary check (Kyoto, Shimanami Kaido, Yakushima and Tokyo)

Me and my partner are planning a 24 day trip to Japan. It’s our first time. We’ve done some research and decided that what we want to do is: 

  • spend a few days in Kyoto with a day trip to Nara, rent a car in Kyoto for 2 or 3 days and explore the Kii Peninsula (including some hiking)
  • bike the Shimanami Kaido trail
  • MAYBE squeezing in one or two days in Kyushu (Mount Aso and/or Takachiho Gorge)
  • spend a couple of days in Yakushima island 
  • spend a couple of days in Tokyo at the end of the trip

Seems doable to me, but maybe I’ve not taken enough factors into consideration. Please advise! Below the detailed itinerary: 

31 Oct (Thursday): 

Arrive at Haneda Airport at 2:30 PM, take a train to Kyoto. We don't have any luggage to pick up and our hotel in Kyoto is close to the train station. expecting to arrive at the hotel in the evening.

1 Nov (Friday) – 8 Nov (Friday): 

8 full days in Kyoto:

  • explore Kyoto
  • rent a car for 2 or 3 days to explore the Kii Peninsula, maybe with an overnight Kumano Kodo hike, if not – just some day hikes.
  • trip to Nara – either as a day trip by train, or by car since we're renting it anyway; or considering renting bikes in Kyoto, bike to Nara and stay for the night and bike back to Kyoto the next day (please advise here!)

9 Nov (Saturday): 

Train to Onomichi in the morning. easy afternoon and evening in Onomichi.

10 Nov (Sunday) – 11 Nov (Monday):

Rent bikes in Onomichi; 2 days biking the Shimanami-Kaido, with an overnight stay in Setoda; return bikes in Imabari; stay overnight in Imabari.

12 Nov (Tuesday):

Early morning bus from Imabari to Onomichi, train to Fukuoka, flight to Yakushima. arrive in Yakushima at 2 pm, take a rest and enjoy the rest of the day. Staying in Miyanoura.

13 Nov (Wednesday) – 16 Nov (Saturday)

Four full days in Yakushima with a rental car. Hiking, snorkling, get to the underwater onsen during low tide, hoping see some turtles 🙂

17 Nov (Sunday)

Flight to Kagushima and then Tokyo, arrive at Haneda at 1 pm. Taking it easy. Staying in Asakusa, exploring the neighbourhood a little in the evening.

18 Nov (Monday) – 23 Nov (Saturday)

6 full days in Tokyo.

Exploring the city, visiting some museums, considering a day hike at Hatonosu Valley or Mitake and Odake mountains, as we've heard they're year-round hikes.

24 Nov (Sunday)

Half a day in the city and flying back home from Haneda Airport at 10 pm.

We want to do Tokyo last, as we want to bring some nice things home and don't want to travel with it the whole trip (we arrive in Japan with hand luggage only, but depart with registered luggage). Taking that into consideration, I assumed the order: Kyoto > Shimanami Kaido > Yakushima > Tokyo makes the most sense, as we can save some time (and money) by taking one long flight at the end of the trip (Yakushima to Tokyo). I think it also makes sense considering the autumn foliage, right?

We're wondering if squeezing in a day or two in Kyushu to do the Mount Aso hike and/or rent a boat at Takachiko Gorge is too much? That would mean a day or two less in Kyoto or Tokyo. It also seems like a lot of hustle (renting a car in Kagushima probably, lots of driving in little time). Would you say it's worth it? We're always quite active on our vacation and you can probably already guess we love nature, but we don't want to just cross things off the list at any cost.

We've checked the flight schedules and checked the trains with google maps.

I'd appreciate any comments, suggestions, remarks. Thank you!

by Narrow_Tea_9337

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