The station was planned as part of the construction of IND and BMT's Archer Avenue Line as outlined in the Program for Action in 1968.

Bids on the station's construction were received on July 9, 1982, and the contract was awarded to Carlin-Atlas Corporation for $17.91 million.

Work on the station started on July 15, 1982,[4]: 14  and opened along with the rest of the Archer Avenue Line on December 11, 1988.

[7] 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.

[12] The MTA announced in December 2021 that it would install wide-aisle fare gates for disabled passengers at five subway stations, including Sutphin Boulevard, by mid-2022.

[citation needed] As with other stations constructed as part of the Program for Action, the Sutphin Boulevard–Archer Avenue–JFK Airport station contained technologically advanced features such as air-cooling, noise insulation, CCTV monitors, public announcement systems, electronic platform signage, and escalator and elevator entrances.

[4]: 14  The station's mezzanine is located above the IND platform under the intersection of Sutphin Boulevard and Archer Avenue.

[32][25]: 17.3, 17.4  The two northern staircases go down to an unstaffed fare control area, which as of 2007[update] consists of four High Entry-Exit Turnstiles.

[25]: 17.3  On the southeast corner, two escalators (one up, one down) and a staircase lead to street level, just outside the Long Island Rail Road (LIRR)'s Jamaica station.

Three elevators provide access to the street level and the LIRR station's main mezzanine areas.