Nassau Street Shuttle (1999)

This shuttle ran only from May to September 1999 during the rehabilitation of the Williamsburg Bridge. The shuttle ran from 6:00 am to 10:00 pm daily from Essex Street to Broad Street (Chambers Street on weekends, late nights, and evenings).

Myrtle Shuttle (2017–2018)

Two trains operated separately on each of two tracks on the BMT Myrtle Avenue Line between Myrtle-Wyckoff Avenues and Middle Village-Metropolitan Avenue. They ran at all times between September 2, 2017, and April 27, 2018, due to construction on the BMT Myrtle Avenue Line's connector with the BMT Jamaica Line.^[5] It was designated as an orange "M" on maps, schedules, and station and service notice signs, and as a brown "M" on the R42 rolling stock, which still had the brown "M" emblems that the route used before 2010.

Lenox Shuttle (mid-1900s – early 1970s)

The Lenox Terminal Shuttle (also Lenox Shuttle and Lenox Avenue Shuttle) ran between 148th Street and 135th Street when the 3 did not run. Prior to the opening of the 148th Street station on May 13, 1968, it was called the 145th Street Shuttle, running only to 145th Street, and only from 9:00 pm to 1:00 am. It was in place by 1918,^[6] but may have been started in 1905 when the IRT White Plains Road Line opened to the IRT Lenox Avenue Line.

Between 1969 and 1972, it was folded into the 3, but continued to run as a shuttle at those times. Late night 3 service ended on September 10, 1995,^[7] due to low ridership,^[8] and was not restored until July 27, 2008. During this time, the route was served by a free overnight shuttle bus.^[9]

Myrtle Shuttle (1969–1973)

After the BMT Myrtle Avenue Line south of Broadway ceased operation on October 3, 1969, the MJ service was discontinued and the current nighttime M shuttle was formed, using the lower-level platforms in the same station complex. Prior to 2014, when the M was extended to Essex Street during weekend days, it operated on weekends as well. However, this service was labeled SS and considered a separate route from the M until the two routes merged in 1973.

Bay Ridge Shuttle (1990–2002; 2004–2016)

On September 30, 1990, late night R trains began operating as a shuttle in Brooklyn, between 36th Street (cut back from 57th Street in Manhattan) and 95th Street.^[10] In 1999, northbound trains began skipping 53rd Street and 45th Streets to avoid discharging passengers on tracks used by through trains. From September 8, 2002, until February 22, 2004, this service was extended northward to Pacific Street, due to reconstruction of the Coney Island station, running express north of 36th Street. On November 5, 2016, late night R trains were extended to Whitehall Street in Lower Manhattan.^[11]