The station was not originally proposed as part of the Program for Action in 1968, but a later revision to that plan entailed building a Second Avenue Subway with one of its stops located at 96th Street.

Since opening, the presence of the Second Avenue Subway's three Phase 1 stations has improved real estate prices along the corridor.

The Second Avenue Line was originally proposed in 1919 as part of a massive expansion of what would become the Independent Subway System (IND).

[13] As part of the New York City Transit Authority's 1968 Program for Action, the construction of the full-length Second Avenue Subway was proposed.

[17] Many community representatives requested that a station, in addition to those already proposed, be constructed in the vicinity of 96th Street and Second Avenue, principally to serve the Metropolitan Hospital which provides medical service to large numbers of low-income patients.After considering the testimony presented at the hearing, the New York City Transit Authority adopted a resolution providing for the construction of a station at 96th Street at a cost of approximately $10,000,000.

[15]All Second Avenue Subway stations built under the Program for Action would have included escalators, high intensity lighting, improved audio systems, platform edge strips, and non-slip floors to accommodate the needs of the elderly and people with disabilities, but no elevators.

[18] The stations were to be made with brick walls and pavers alongside stainless steel, and would have relatively small dimensions, with 10-foot (3.0 m) mezzanine ceilings.

[19]: 110 A combination of Federal and State funding was obtained, and despite the controversy over the number of stops and route, a groundbreaking ceremony was held on October 27, 1972, at Second Avenue and 103rd Street.

[27][28] The line's first phase, the "first major expansion" to the New York City Subway in more than a half-century,[29] included three stations in total (at 72nd, 86th, and 96th Streets), which collectively cost $4.45 to $4.5 billion.

[40] The forced evacuation of two buildings near the 96th Street station delayed the contractor's plan to use controlled blasting to remove bedrock in the southern section of the launch box.

[42][43] Earth excavation was conducted between walls once they were installed, and box structures were built using a bottom-up construction method.

[46] On March 19, 2013, a construction worker got stuck in waist-deep muck at the station site;[47][48] he was extricated after four hours of rescue efforts, but nearly died after the incident.

[70] Its design was likened to a Washington Metro station by Michael Horodniceanu, President of MTA Capital Construction.

[74][75] As with other stations on the first phase of the Second Avenue Subway, it was designed and engineered by a joint venture of Arup and AECOM.

[82] According to an internal study prepared for the MTA in 2020, the 96th Street station could theoretically accommodate half-height platform edge doors.

Full-height platform screen doors would be possible but would necessitate the installation of structural bracing and relocation of several mechanical systems.

[88] In 2009, MTA Arts & Design selected Sarah Sze from a pool of 300 potential artists to create the artwork for the station.

[89][90] Her work, which was created by Spanish artisans Alcalagres,[90] consists of blue, violet, and lavender landscapes,[91][89] as well as depictions of wind blowing things around.

[92][90] A New York Times reporter described it as "fragmented images of scaffolding, birds, chairs and leaves, digitally collaged.

The work also serves the practical purpose of helping navigation, as the sheets are more closely packed together near the exits than in the middle of the station.

Each entrance features a different shade of blue and a blueprint-style vector line design, a visual theme that is integrated with the architecture.

To illustrate the area's transitional condition, the writer stated that the 96th Street station was situated within a few blocks of a high-crime housing development on First Avenue, an old ice-skating rink frequented by "squeegee men" who would demand money from drivers, a tenement where future President Barack Obama lived in the 1980s, the Islamic Cultural Center of New York, as well as the Mayor of New York City's residence at Gracie Mansion.