Flushing served as the terminus of the NY&F until October 30, 1864 when a subsidiary known as the North Shore Railroad extended it to Great Neck, and it was burned in order to prepare for a second station that was built between January and February 1865.

Shortly after the line was electrified on October 22, 1912, the station was abandoned on November 11, 1912, as part of an effort by the Long Island Rail Road to bring the Port Washington Branch above and below street level depending on the location.

A one-story commercial building on the west side of Main Street was demolished and replaced by a station house with an elevator, which provided more direct access to the westbound platform.

[5] On October 28, 2013, the MTA held a public hearing on the proposed acquisition of private property at 40-36 Main Street in Flushing for the purpose of adding an elevator intended for the rebuilt station.

In addition to connecting with the nearby subway station of the same name, Flushing–Main Street serves as a major bus-to-rail interchange in Queens, with over 20 bus routes running through or terminating in the area as of 2015[update].