If you have a 7-day Japan Rail Pass, you can avail of unlimited rides on the JR train lines around Japan and reserve seats for free in a span of 7 days. The following is an itinerary that you can follow to make good use of your 7-day JR pass:
Day 1 Narita Airport to Tokyo:
Upon arriving at Narita Airport, you can exchange your Japan Rail Pass voucher at the JR East Travel Service offices found at both Narita Airport’s Terminal 1 and Terminal 2. Ask for the pass to be activated on that day so that you can use it to get on the JR Narita Express to go to Tokyo. The trip takes about one hour.
Day 2 Tokyo:
Start your Tokyo sightseeing with a visit to Tsukiji Market early in the morning. To go there using your JR Pass, take the JR Yamanote line to Shinbashi Station and walk 20 minutes to the market.
Next stop is the Imperial Palace, which can be accessed via the JR Yamanote and the JR Keihin-Tohoku Lines. Upon getting off at Tokyo Station, take a 10-minute walk to the palace grounds.
Spend the rest of the day exploring the electronic and otaku district of Akihabara, which is only two stops away from Tokyo Station; and/or the Ueno area, which has a spacious park with temples (Kaneji, Kiyomizu Kannon), shrines (Toshogu), museums (Tokyo National Museum, National Science Museum, Tokyo Metropolitan Art Museum), and a zoo (Ueno Zoo).
Day 3 Tokyo to Kyoto:
With a JR Pass, you can take a Shinkansen from Tokyo Station going to Kyoto Station. The one-way journey takes about two hours and 40 minutes.
Upon arriving in Kyoto, you can immediately begin your sightseeing, particularly around the train station, where attractions such as the Nijo Castle, Nishiki Market, Kyoto Manga Museum, Kyoto Aquarium, and Kyoto Aquarium can be found.
Day 4 Kyoto:
In the morning, hike up to the Fushimi Inari Shrine (a round trip takes between two and three hours), and then spend the rest of the day in Eastern Kyoto to visit the Kiyomizudera, Ginkakuji, Nanzenji, Kodaiji, Eikando, and other world heritage temples and shrines in the area. If you have more time, throw in a few hours for Northern Kyoto, where you can see more cultural sites, such as the Kinkakuji, Ryoanji, and Hieizan temples.
Day 5 Kyoto — Day trip to Nara:
Because Nara is only about an hour’s train ride away from Kyoto, you can make it a day trip and visit the Todaiji Temple, Heijo Palace, Yakushiji Temple, Kofukuji Temple, Nara Park, and several other historical and cultural sites in the city. Your 7-day JR Pass will come in handy as it is valid on the JR Nara Local and Rapid Service trains that directly link the two cities.
Day 6 Kyoto — Day trip to Osaka:
From Kyoto, taking the train to Osaka takes only about half an hour via the JR network. Depending on your interests, you can spend the entire day in Osaka either at theme parks (Universal Studios, Osaka Aquarium); the city’s historical landmarks (Osaka Castle, Sumiyoshi Taisha, Shitennoji Temple, Tenmangu Shrine); the museums (Museum of History, Science Museum, National Art Museum); or the shopping districts (Shinsaibashi, Namba, Den Den Town, Grand Front Osaka).
Day 7 Kyoto to Narita Airport:
On your final day in Japan, you can use your JR Pass to make your way back to Narita Airport. From Kyoto Station, you can get on a Shinkansen to Shinagawa Station and then transfer to the Narita Express Line. The entire trip takes about two and a half hours.