Port Jefferson is the terminus for the Port Jefferson Branch of the Long Island Rail Road. The station is located on New York State Route 25A (Main Street), on the north side of the tracks, but is also accessible from Oakland Avenue, as well as Railroad Avenue and Union Street on the south side of the tracks in Port Jefferson Station. All service is diesel-only, and most off-peak trains are shuttles requiring a transfer to an electric train at Huntington or Hicksville.