The Port Jefferson Branch is a rail line and service owned and operated by the Long Island Rail Road in the U.S. state of New York. The branch splits from the Main Line just east of Hicksville and runs northeast and east to Port Jefferson. Several stations on the Main Line west of Hicksville are served primarily by trains bound to/from the Port Jefferson branch, so LIRR maps and schedules for the public include that part of the Main Line in the "Port Jefferson Branch" service.

The Main Line is a rail line owned and operated by the Long Island Rail Road in the U.S. state of New York. It begins as a two-track line at Long Island City station in Long Island City, Queens, and runs along the middle of Long Island about 95 miles (153 km) to Greenport station in Greenport, Suffolk County. At Harold Interlocking approximately one mile east of Long Island City, the tracks from the East River Tunnels and 63rd Street Tunnel into Manhattan intersect with the Main Line, which most trains use rather than using the Long Island City station.