With the Japan Rail Pass, you can ride on all JR trains, including the Shinjuku Line, without paying additional fares. However, it's important to note that the Japan Rail Pass is not valid on other non-JR train lines, such as private railways or subways.

This is a common point of confusion for Tokyo travelers: the answer depends on which "Shinjuku Line" you mean. The Toei Shinjuku Line (a subway line with the 'S' logo) is not covered by the JR Pass because it is operated by the Tokyo Metropolitan Government, not Japan Railways. However, the Shonan-Shinjuku Line is a JR-operated heavy rail line that connects Shinjuku to places like Yokohama, Kamakura, and Saitama, and it is fully covered by the JR Pass. Additionally, many other JR lines pass through Shinjuku Station, such as the Yamanote Line, Chuo Line, and Saikyo Line, all of which are covered. If you accidentally enter the Toei subway gates with your JR Pass, it won't work, and you'll need to use a Suica or Pasmo card. A good rule of thumb in 2026 is to look for the green "JR" logo; if it's there, your pass is good to go. If you see the Toei or Tokyo Metro logos (circles with 'S' or 'M'), you'll need to pay a separate fare.