The Cross Island branch began in 1955 as an extension of the Central Queens branch, which had been a fixture in the Jamaica part of the borough since 1917. The impetus for establishing YMCA programs came in part because of increasing youth delinquency, leading local business owners and members of service organizations to advocate for the expansion of YMCA programs as a means of combatting teen violence. The Central Queens branch agreed to assist, and the Eastern Queens branch opened in a donated storefront on Springfield Avenue in Queens Village, with limited professional staff and help from local churches and schools.

The shoestring operation was instantly successful-- so much so that plans for a building emerged not long after the branch began operations. A purpose-built building wasn't opened, however, until 1965. Located at 238-10 Hillside Avenue, in the Bellerose neighborhood, the new branch was located on land purchased from the State of New York. Despite its new building, Eastern Queens retained its status as an extension of Central Queens until 1974.

In 1979, the YMCA once again acquired state land adjacent to the building when Jack Kleinoder, a longtime supporter of the Eastern Queens branch, made the purchase on behalf of the YMCA. Fundraising for an addition began in 1983, with Mr. Kleinoder taking a leading role, and a significant addition to the 1965 building, named after the branch's benefactor, was opened in 1987. The addition allowed the branch to strengthen its focus on accessibility, which included nationally recognized swimming and other programs for disabled children and adults. In 1989, the branch name officially changed to the Cross Island Y and in 1991 was designated an aquatic training center for the Special Olympics.