Looking for suggestions on upcoming Japan trip

Too bad you can't do more time in Japan is it special.

Kyoto is a MUST see, it is amazing. We took a local three day tour that had us on the high speed train from Tokyo.
We had three days in Kyoto and Nara (did the tame deer park that was special).
Kyoto wasn't bombed in WWII and has a lot of intact ancient stuff to see. Do your research and try to visit the best places. You can't walk to all the places, you need transport. We were on a tour so, no problem.
We did do the Philosopher's Walk one day. That was nice.

Do not miss the Golden temple (not sure the exact name)/
https://www.tripadvisor.com/Attraction_Products-g298564-a_contentId.1175378777810163+268262891-Kyoto_Kyoto_Prefecture_Kinki.html

One place I really enjoyed in Tokyo was Team Lab Planets. https://www.teamlab.art/e/planets/
You need to buy tickets in advance for this.

When you are thinking about lodging, start by thinking about which airport you will be flying into. Will you be flying into Narita or Haneda? Look for hotels that are easily accessible from the airport and have major public transport connections to them.

If coming into Haneda, Hotel Oriental Express Tokyo Kamata is on a direct train line from the airport. Just a few minutes from the Station with plenty of shopping, grocery, restaurants, and convenience stores nearby. https://tokyokamata.hotelorientalexpress.com/en/

You will want to preload a Suica card on your phone. You will use this for transportation and most purchases. Easy to add money to it as needed. https://www.jreast.co.jp/en/multi/pass/suica.html

You will love Japan and want to come back!

I share your focus on food. We've had quite the incredible visits to Japan, most recently in 2019.

I have to dig up some restaurant names, but one I do remember the we liked very much, was SHIMA STEAK in Tokyo. Very tiny, family-run place. We had lunch there and brought one of their famous steak sandwiches to the Do-me for a baseball game.

One of the best restaurant was one specializing in pork tonkatsu...hidden in an office building and seating about 6 diners at the counter....if you want, I can try to dig up the name. There are entire website devoted to the tonkatsu restaurants in Tokyo..the Japanese take obsession about food to an entirely new level!!

Use Tabelog for restaurant reviews in Japan, and have your hotel make reservations.

https://tabelog.com/en/

Highly recommend going to the Tokyo Dome, even if you do not care much about the game...it's the crowd, and the vendors, that were fascinating. We stayed in the ShangriLa near Tokyo Station and Ii thought that was an excellent area to base oneself. Inside the station there is a riot of small restaurants, so on the nights when we did not book a restaurant, we wandered inside there and had a blast....

In Kyoto, we took advantage of the services of a GoodWill Guide, a volunteer who will craft a plan based on your interests, and accompany you for the day. You pay only for the guide's lunch. Be aware that the English fluency of the guides varies.

https://www.japan.travel/en/plan/list-of-volunteer-guides/

We took a Tokyo food tour with Yukari Sakamoto, Japanese-American woman (her husband was a buyer at Tskujii Market) who has written several respected food guides to Japan; -she took us on a private tour based on our particular interests..

https://about.me/yukarisakamoto

This is her book; highly recommend:

https://www.amazon.com/dp/189214574X?lv=shuf&channelId=500&plpRedirect=mhFallback

For your son,, you must go to Harajuku..enough said.
We also loved the neighborhood where they sell the cookware and those plastic molds of food that some restaurants put on view....

I think you know about the cute animal cafes....devoted to every animal from hedgehogs to capybara....

We went on our own, no tour necessary....we had about a week in each of those two cities; two nights in Kanazawa (forr the gardens) ; and an overnight at an onsen hotel (KAYOTEI) in Yamanaka Onsen; if you can squeeze this in, it's an incredible exprerience.. we chose KAYOTEI because we had a private bath on the terrace of our room, which my partner preferred. All meals are Japanese and no English is spoken so it was quite the experience!!!! Not sure you have time on this trip, but it's an idea I wanted to share because it was so special...

https://blog.bespoke-discovery.com/anniversary-guide-to-kayotei-ryokan-yamanaka-onsen-privacy-and-surprise-design

Recommended book about food: RICE, NOODLE, FISH: DEEP TRAVELS THROUGH JAPANS FOOD CULTURE

You probably know this, but you can send your bags ahead on the train and pick them up at the airport on the day you fly out of Japan..

We are flying into and out of Haneda.

Lived in Japan many years, and return annually. Trip report for a part of Tokyo might be useful reference:
https://community.ricksteves.com/travel-forum/trip-reports/trip-report-japan-tokyo

Since you settled on Tokyo 🗼 I suggest staying near anywhere you can easily walk to two different subway lines since that is the primary way you will get around. I would probably avoid kabukicho (sorry it's gross late at night) and maybe rapponggi. Stick closer towards Shinjuku or the other side near the museums and stadiums. The airport is very far away from the downtown fun bits- i wouldn't bother staying near it. Tokyo is really good for day trips. To be honest since you trip is so short i would drop Kyoto from the itinerary. Kyoto is my favorite place in Japan but it takes about 3+ hours when you factor running around with your luggage and finding the right train and whatnot. Don't bother. Tokyo can have great day trips to Kamakura and Ibaraki. The hitachi seaside flower park is in full bloom with different plants depending on time of year and anyone can enjoy it (it was literally the best day trip I had in my two weeks in Japan). Kamakura has many ancient sites and it's a perfect day trip. As for food Tokyo has dozens of great restaurants. Check on hotpepper or similar sites that are in Japanese. If it's a 3+ rating it's more like a 5 star here because they generally locals don't give any place 5 stars. Kyoto is great but you will feel rushed and prob be stuck seeing things when it's tourist hell time. It's best at 6am or 9pm. Otherwise it's very crowded and not as much fun.

Regarding the hotel, I fully intend for us to stay in a neighborhood, close to subway stops, but there are so many neighborhoods, not sure which ones I should be focusing on when I search. We tend to be budget travelers (although now that we are getting older, less budget than we used to), but definitely not going to be choosing any five star hotels. My philosophy has always been, as long as it is a comfortable place to stay, why spend extra when you are going to be in the hotel for so little time anyway. Definitely need a comfortable bed - with my back and knees, no sleeping on the floor on a futon any more.

I echo the recommendation of teamLab Planets. Your son will probably love it. Two of our guides recommended it to our son, and my husband and I loved it as much as he did. We only got our tickets a few days in advance (late March 2026), but we didn’t have a lot of choice on the times. We ended up going on a Saturday night, which worked about fine. TeamLab has another museum in Tokyo, but we didn’t go so I can’t tell you which is better.

I’m guessing you have the Ghibli Museum on your list since your son loves anime. This is another place we went because my son really wanted to see it. Again, all three of us loved it. It is very difficult to get tickets. I actually watched two videos on how to do it, which helped enormously. Plan to have multiple phones/PCs logged in at the appointed time so hopefully one will get a low number. Tickets go on sale at 10 am on the tenth of each month for tickets the following month.

I would suggest four nights in Tokyo and three in Kyoto so you have more time in Kyoto. There are a lot of shrines and historic sites to see. You don’t need to see them all; a sampling is good. I really liked Fushimi Inari, Nijo Castle, the Gion District, Ginkaku-ju Temple (the Silver Pavilluon), and Kiyomizu-dear Temple. Kodai-ji Temple in the Gion District is nice because it has a small bamboo forest and is in the Gion District, so easy to get to. The large bamboo forest is much farther and will take up too much of your time.

In Tokyo, you should consider Asakusa Shrine and Kaishikawa Karakuen Garden, as well as Hie Jinja, for a taste of old Tokyo. Shibuya Crossing is fun to see, and I would definitely go up high for an amazing view of Tokyo and if you are lucky Mount Fuji. The Tokyo Metropolitan Government Building is free, so no need to pay a lot for the view.

If you like museums, the Tokyo National Museum is very nice, but I wouldn’t call it a must see. Unfortunately , the Edo Museum was closed when we were there.

I kind of liked wondering through the different neighborhoods as much as any particular site, except for the Ghibli Museum and teamLabs.

We are not shoppers either, and I wouldn’t feel like you have to shop. But wandering through the Sunshine City shopping mall, was kind of fun.

We are not foodies, so I can’t help you with food. However, I will tell you we did not have a bad meal the entire time we were in Japan.

I wasn’t expecting to like Japan as much as I did. It is fascinating!

Just wanted to add that the suggestion to skip Kyoto in lieu of one or two close day trips is not a bad idea. You will save a lot of transit time, which is critical on a short trip. Kyoto has some very cool things to see, but the city is surprisingly ugly. The pretty parts and the historic buildings are extremely crowded, much more so than Tokyo. Tough decision.

Hi, Great you can fly in & out of Haneda, much closer to town. I lived in Tokyo for 7 years decades ago, but I was back for a visit in 2028. We stayed at Mitsui Garden Hotel in Gotanda, it was around $150 per night, breakfast was AMAZING and the service was equally wonderful. Maybe a 3-star, impeccably clean & on the top floors, great view from the lobby. It's right next to the Yamanote line so great choice for grabbing trains.

IF you do decide to stay there, LMK & I will look up an amazing 'Farm to Table' restaurant next door in a nondescript shopping arcade. Gotanda is on the Yamanote circle line above ground, will get you around Tokyo & connects to the subway system, and it's nice to be above ground & see the views. Agreed, get the Suisa card, it will save you a lot of hassle as many train lines are privately owned and figuring out the tickets can be a hassle.

If you do go to Harajuku, avoid Sundays as it will be jammed. And my love of Asakusa Shrine over the years has dimmed due to the crowds, after braving the crowds, we visited Nezu Shrine, we were the only non-Japanese there, most were pilgrims. If you go on a weekday it will be quieter.
https://www.japan-experience.com/all-about-japan/tokyo/temples-shrines/nezu-shrine.

My favorite excursion from Tokyo is to Kamakura, rent a bike at the train station, first bike to Hokokuji temple, it has an ancient bamboo forest & a green tea hut where you can sit and look out at the garden.https://www.japan-guide.com/e/e3120.html.

When you get into a taxi, don't close the door, the taxi driver has a foot pedal to close it and it hurts his foot if you do it! Enjoy, Japan is utterly delightful and utterly different,

Kyoto is wonderful but 2 nights is not enough in my opinion. When I was in Tokyo for a conference, it was suggested that people who wanted to travel after the conference but didn't have enough time to go to Kyoto might consider a daytrip from Tokyo to Kamakura. I know people who did that and felt it was worthwhile. I was fortunate to have a couple weeks to travel around.

I have a question about Suica. I notice several people mentioning using their phone for Suica, but when I went to the web site, all I saw was references to a physical card instead of it residing on a phone. I assume there is a specific app you have to get? But I am r the web site doesn't mention it. (I actually am a little more comfortable with a card because I am always worried that something will not work right with the phone, although just using the phone can be more convenient.).

I seem to recall it was a physical card (in 2018) similar to the old London Oyster card, you top it up at any major station. We bought ours when we arrived into Narita.

What irony.... I've spent the better part of the day on details of my fall 2026 trip. Not my first to Japan.

I won't repeat the suggestions above - but note: Edo-Tokyo Museum has re-opened if that is of interest.
If the suggestion is there I missed it - look into Nikko as a day trip. Options to focus on nature or history or both.

I would suggest skipping Kyoto fully if Tokyo holds more interest. OR - skip Tokyo if your research seems to show Kyoto is more of personal interest. There isn't time for both - as has been said above. (Of course, if it's your only trip for the foreseeable future, you may decide one full day, 2 nights as you are considering is better than none - look at the Navitime or Jordan apps to see train schedules. For myself, I'd give Kyoto more time than Tokyo.)

I used a Suica on my phone last trip, about 12 months ago. It worked well. I could add money while standing on the platform waiting for a train. I'll be using it again this trip. As for the websites with references for physical cards, they are still available if you prefer this. Either works.

I have an iPhone - click on the wallet "+" , then hit Transit and Japan's options will appear.

PS - I was a bit stunned at hotel prices vs my last trip.............. I would be looking for September now.

I noticed an autocorrect on my post above.

The two very good travel apps for researching Japan's train routes, schedules, and cost are: Navitime and Jorudan. Autocorrect wants me to type "Jordan" - there is a "u" in the middle.

I use both when using local transport around Tokyo and want metro info as well as for distance travel. I've never had one or the other steer me wrong. Apple Maps works well for walking routes.

Japan Guide is a good website for ideas and info on sites. Tokyo Cheapo, Japan National Tourism Organization and for Kyoto, Inside Kyoto. I haven't looked at a physical tour book for Japan for multiple years, but I do remember that the info was sometimes more dated than seems typical - be sure to check websites for any place you want to visit. There are a lot of random closing dates for museums - changing exhibits, obscure holidays, etc.

You can get a physical Suica card though I have it loaded on my phone as I find that a bit more convenient.

You can go to the JR East web site Suica page - https://www.jreast.co.jp/en/multi/pass/suica.html - or to your phone's app store for info. Though not sure if it is available for Android phones. I have it on an iPhone.

One of the nice things about having it on the phone is you can add money easily if you need to. On my trip earlier this month, I ran low and added money while in transit in Tokyo. Some like having the card as it becomes a souvenir.

You may also be able to just use your credit card at some stations. That process is coming into more common use but I don't have any experience with it as I am in the habit of using Suica on my phone.

Suica is accepted outside of the JR East region but not everywhere. I have used it on JR West so think you could use it in Kyoto but am not completely positive on that.

You can use Suica in Kyoto.

Basically, the IC cards can be used within a region, but not cross-region - for example, you cannot use to travel by distance train from Tokyo to Kyoto. There are also a few small "trunk line" routes where it is not accepted, despite being with a region. Express trains even within a region can have different rules. This is a broad summary - there can be exceptions.

This is much more info than the OP will need. For his purposes, Suica or other IC cards can be used in Tokyo and Kyoto. Separate train ticket must be purchased for distance travel.
https://www.japan-guide.com/e/e2359_003.html

I just remembered that 2 years ago, I took a younger relative, who was slightly older than your son, to Tokyo. He requested a visit to the Akihabara area - known as Electric Town. Not my interest, so this area was new to me although widely touted in the tour guides.

I have to say, I had a lot of fun. We were there probably only 90 minutes - 2 hours not counting the lunch we had.