[13]: 15  Construction on Section 7 of Route 131D, the Southeast Queens Line, which included the Jamaica–Van Wyck station started on October 17, 1979.

[16][15] It serves as the replacement for the former Metropolitan Avenue and Queens Boulevard stations of the BMT Jamaica Line.

[18] In 2020, the MTA announced that it would reconstruct the track and third rail on the IND Archer Avenue Line, which had become deteriorated.

From September 19 to November 2, 2020, E service was cut back to Jamaica–Van Wyck, with a shuttle bus connecting to Sutphin Boulevard and Jamaica Center.

[25] As with other stations constructed as part of the Program for Action, the Jamaica–Van Wyck station contained technologically advanced features such as air-cooling, noise insulation, CCTV monitors, public announcement systems, electronic platform signage, and escalator and elevator entrances.

On the Manhattan-bound side, the station walls contain spaces for skylights to allow natural sunlight in,[23] but they are currently covered over.

[14] One entrance is at the southwest corner of Van Wyck Expressway and 89th Avenue next to Jamaica Hospital Medical Center.