In 1948 the New York City Housing Authority (NYCHA) and the East Harlem Council for Community Planning assembled a coalition of community service organizations and settlement houses to develop social service programs for residents of the newly opened James Weldon Johnson Houses. This “Headworkers' Council” included representatives of Union Settlement, Casita Maria, 110th Street Community Center, The Junior League, Girl Scouts of America, and Community Service Society. These agencies provided funding and staff to establish recreation, education and group work programs at Johnson Houses in rent-free space provided by NYCHA. Mildred Zucker, a social worker who had volunteered at Madison House during the 1930s, was paid by the Community Service Society to coordinate the work. In the following year a board of trustees was recruited, and James Weldon Johnson Community Center, Inc. (JWJ) was independently incorporated. Board members included Lewis Isaacs, son of City Council member Stanley M. Isaacs; Bert Beck of the Community Service Society; and William Kirk, Headworker of Union Settlement. In 1952 JWJ formalized its identification with the settlement house tradition by joining United Neighborhood Houses, the umbrella organization of New York settlements.

The problems of juvenile delinquency and gang activity among East Harlem teenagers were of primary concern to the new agency. JWJ staff reached out to neighborhood young people by forming a “Teenage Committee on Narcotics.” In 1959 JWJ worked with the Youth Committee of East Harlem to establish a Youth Employment Service providing vocational guidance and job placement for teenagers. Other programs established at JWJ in its early years were clubs, athletics, and scout troops for children, and classes in english, sewing and carpentry for adults. In 1953 JWJ became a pioneer among settlement houses by launching a mental health clinic. Staff psychiatrists met with children, teens and adults referred by JWJ group workers and NYCHA staff. The Monticello Day Care Center was opened under JWJ auspices in 1955; that same year the settlement broadened its area of service by sponsoring a community center in NYCHA's new Jefferson Houses.

In response to the ongoing construction of public housing in East Harlem, JWJ and Union Settlement Association established in 1957 the East Harlem Project, which sought to involve community residents in the urban renewal process. Under the leadership of Ellen Lurie, the project fostered citizen participation in planning schools and housing, and conducted a consumer education campaign which led to the formation of a JWJ credit union.

The expansion of cultural programs was a major focus of JWJ's work during the 1960s. The settlement co-sponsored outdoor concerts and dance performances at East Harlem Plaza, a public space designed by architect Albert Mayer with input from Mildred Zucker. In addition, JWJ offered classes in theater, dance, visual arts and sound recording at its new Theater Arts Center, built by NYCHA. The Theater Arts Center sound studio was later used in an innovative program to train young people for careers in record engineering.

During the late 1960s many East Harlem residents demanded greater community involvement in the planning and administration of JWJ programs. The composition of the settlement board and staff, and the location of its programs were questioned by neighbors, prompting the settlement to re-examine its mission. In the fall of 1967 Mildred Zucker proposed to a staff conference that “... we must help our neighbors to take over systematically those services which we now operate, as they become prepared to take them over, and we must train them to assume this new responsibility.” During the next several years, the JWJ Board of Directors supported this initiative by recruiting East Harlem residents to board membership, and by hiring a community resident, Rafael Ferrer, to replace the retiring Mildred Zucker as Executive Director.

During the 1970s and '80s JWJ activities focused on the youth of East Harlem. Day care, Head Start, the Revive drug prevention program, and a community library were run by the settlement under increasingly difficult financial conditions. Other JWJ programs were discontinued during this period, or were taken over by other agencies. In the 1990s JWJ continues to serve the East Harlem community under the leadership of Executive Director Natalie Williams.