My boyfriend and I booked a spontaneous (3 weeks before going) trip to Japan last November. We didn't have much time to plan, so I immediately started after we booked our flights. I knew very little about what we wanted to do or see, but knew I needed to start somewhere if we were going to get the most out of our week in Japan.
Step 1: Decide where you want to go
I knew at the very least I wanted to visit Kyoto and Tokyo. These are two cities everyone should visit on their first trip to Japan. A week is not a lot of time, so you'll need to decide if you want to see as much as possible or take it slow. If you're taking it slow, then I'd suggest 3 days in Kyoto and 4 days in Tokyo. I wanted to pack in as much as possible because I always try to cover all the bases on my first trip to a country. I like to get a lot of the small things checked off, so when I return I can take my time exploring the lesser known parts. If you want to see as much as possible then I'd suggest:
1-2 days at a Traditional Ryokan in Hakone
3 days in Kyoto (Day trip to Osaka and Nara)
4 days in Tokyo (Day trip to Yokohama)
From Kyoto, you can do a half-day in Nara and half (or full) day in Osaka. From Tokyo, there are several day trips, but I would suggest Yokohama for an easy one; it's especially great for families. In Hakone, you can try to see Mt. Fugi if it's nice out by going along the Hakone Ropeway/Cable-car to the lake.
Once you decide on your cities and the number of days, you can begin searching for accommodations. For our trip, we stayed at a Ryokan in Hakone, a Guesthouse in Kyoto, and a Hotel in Tokyo. I would not recommend staying at an Airbnb in Japan. The rumor is they do a lot of last-minute cancellations due to the strict standards that they are held to. Oftentimes, they will cancel to not risk getting shut down. Unless there are high reviews, I'd pass on Airbnb for Japan. Other accommodations are plentiful.
Step 2: Plan Things to Do
After I select the cities, I plan out exactly what I want to do/see in that city. If I can fit enough into the same days and have remaining days, I explore the possibility of day trips. I am a fan of planning out every hour, but I don't hold myself strictly to the schedule, and I deviate from it quite frequently. You spend lots of money and earned time off to travel, so it makes sense to not waste it on planning, which is something you can do from your couch at home.
Step 3: Budgeting and What to Expect
Japan is not really a place for cheap travelers. Sure, there are ways to budget and save money, but it is overall a much more expensive country than other Asian countries (e.g., Thailand, etc.). This is likely because their economy does not depend on tourists. Japanese people already tour their own country a lot, so they don't need tourism as a main industry for their economy to be strong, so you won't see them trying to over-accommodate you or rip you off. The Japanese people are generally very respectful and mindful; that's one of my favorite things about their culture.
Unexpectedly, the food and site-seeing can be quite affordable in Japan. The sushi was also incredibly cheap, you could get several rolls and sake for two people for under $15. For most breakfasts, we either ate at the included breakfast for our stay or we grabbed snacks at the 7-Elevens and hot coffees to-go in the street vending machines. Where I saw most of my money going was towards transportation and accommodations.
Here is a cost estimate for the parts of your week-long trip
Total Budget: ~$3000
Flight: $1000-$1200 - This will depend on where you're flying from. If you have travel rewards points, use them here!
Accommodations: $600-$1200 - This will go down if you're splitting with others and book early. Also if you're flexible, the capsule hotels are extremely affordable in Tokyo. If you're looking to splurge, try the Ryokans, but the best ones will be expensive (but worth it in my opinion)
Food: $300-$400- This depends on your food preferences, but I tend to like to eat out a lot and try all the kinds of foods and get drinks, etc., so my cost could easily be a lot more than yours. If you're planning on Michelin star restaurants, then this budget would increase a lot, of course.
Transportation: $400 - This is assuming you're buying the JR Pass (to ride the futuristic Shinkansens/bullet trains) and Subway rides throughout the trip. Many of the subway rides are very cheap, but after so many they do add up!
Other: $350 - I would say it's safe to budget a lot for extra activities. Many of the sites like temples, gardens, and museums are only a few yen ($3) to visit. However, you'll want to budget for some of the more expensive sites (e.g., Hakone Cablecar, Tokyo Skytree, Robot Restaurant, etc.). I tend to buy lots of souvenirs, but if you're stuck on what to buy while you're there, then just wait until you get to the airport. They have a perfect collection of gifts available at decent prices (e.g., Sake, Mochi, Desserts, Kimonos, T-Shirts, etc.)
Step 4: Transportation
Once you know where you're going, you can start to think about transportation. The JR Pass is a convenient way to get around and it pays for itself if you're using it for travel between Kyoto and Tokyo and a few other small trips on the side (e.g., using the Narita Express when you arrive/depart for the airport) where applicable. When you're in Japan you simply flash the pass to a station worker and they will let you through to your platform. This will not work at the majority of local stations in Tokyo, but you can buy a Suica card when you arrive and just load a ton of money (~$40) on it for the week. You must book the JR Pass in your home country through their site, you cannot buy it in Japan currently.
Step 5: Research, Research, & More Research
I'd love to say I know everything there is to know about traveling to Japan, but I definitely don't! I recommend starting at /r/JapanTravel on Reddit. They have a ton of organized information and you are encouraged to ask for help or submit your itinerary for community review/suggestions. I would start there and as you select the places you want to go, research things to do, and start documenting and prioritizing what interests you. Good luck and feel free to ask me any questions in the comments!
Step 6: Arriving in Japan
I took a nonstop flight from IAD to NRT. Upon arrival, we found an information desk and got instructions to the JR Office. Before doing this, I would suggest picking up your pocket WiFi first since it can be a little bit out of the way to find (located usually on the south/north wings of the airport terminal). Even if you reserved the pocket WiFi through the JR site, you'll still have to pick it up separately. If you're activating your JR Pass when you arrive, then go ahead and ask the attendant to reserve a seat on the Narita Express so you can take that to Tokyo or wherever you're staying.
Last Minute Tips!
Pocket WiFi - This saved us so much time during our trip, plus it was nice to always be connected and being able to look up nearby food, etc. Ours was ~$75 for the full 9 days and you can connect usually up to 10 devices, so you can split this price with however many people are in your group. Either way, it's a reasonable cost and 100% worth it. Bring a backup charger in case it dies during the day!
Learn the Basic Phrases - Contrary to what you may believe, English is not spoken everywhere in Japan. This could be different after the 2020 Olympics, but for now, you'll just need to know a few words to get by: Arigato, Sumimasen, & Kon'nichiwa. At most, you can point to the items you want in restaurants and learn how to use the yen (just move over two decimal points to the left and that's around how much the cost is in USD.
Pocari Sweat - This drink is popular in Korea and Japan. It's their version of Gatorade, but better! You can get them at almost any street vending machine and they help to keep you hydrated and feeling good after 30K-step days!
Use the Coin Lockers on Travel Days - I was hesitant about planning for these because I couldn't find a lot of information on them before our trip. It turns out there are TONS of lockers at many of the stations. At the lesser known ones there are still a decent amount of them. If you're using a 40L backpack you can fit it in the medium lockers or two of your bags in the larger lockers. They actually go back pretty deep. Outside some of the stations (e.g., Hakone-Yumoto) there are coin locker shops where you can also put your bags for the day. Kyoto and Tokyo station had dozens and dozens of lockers, but try to arrive early so you don't have to stress about finding one. For the most part, you will have no issue finding a locker, but these are great so you can do day trips between travel days and not have to carry your bag around! Expect to find these at most stations, we used them at places like Yokohama, Hakone-Yumoto, Kyoto, Osaka, and Tokyo stations.