Shinjuku is a very busy area, with many major train lines and roads running through it, and traffic is heavy at most times of the day, except weekend mornings. Parking is limited to pay parking lots and rented spaces. Shinjuku is the busiest station in Japan, with the highest number of passengers passing through its platforms on any given day. It is the nexus of not only most of the major train lines in Tokyo, but also some of the most important metro lines in the city. JR lines include the Yamanote, Chûô and Chûô-Sobu lines cutting east-west through the city, and the Shonan-Shinjuku and Tokkaido lines heading towards Chiba and Yokohama. Seibu lines go north into Toshima and Nerima wards, and both Keio and Odakyu lines head west and southwest into Setagaya-ku and Meguro-ku, then all to the Yokohama area. Narita Airport is about 90 minutes away via the Narita Express, leaving from Shinjuku station.

Shinjuku-ku is also accessible via the Marunouchi, Shinjuku, Chiyoda and Ôedo metro lines. Highway buses out of the Kanto region leave from Shinjuku station, while local bus services run west into Nakano and Sugnami wards, south into Shibuya, and east into Chiyoda and Bunkyô wards.