The Free Academy was established in 1847 to provide free higher education in the City of New York. In 1961, the City University of New York was established, incorporating the Free Academy and other units under the then Board of Higher Education.

Today the Board of Trustees is the governing entity for The City University of New York, the largest city university system in the world. CUNY is comprised of eleven senior colleges, of which York is one, six community colleges, a graduate school, a law school, a biomedical education school, and a new graduate school of journalism. More than 200,000 students are enrolled at campuses throughout the five boroughs of the City of New York.

On October 24, 1966, the Board of Higher Education of The City University of New York established "Alpha College" as its fifth senior college. Its name was changed to York College by its first president, Dumont Kenny.

York opened its doors in the fall of 1967 in rented space at the Oakland Jewish Center in Bayside, Queens. An entering class of 371 students and a full-time instructional staff of 50 occupied that site for the first academic year. In May of 1968, after hearing presentations from representatives of various Queens communities, the Board determined the permanent location of the College. The successful petitioners were a coalition of business, community and religious leaders advocating for Jamaica, Queens.

While the College awaited its move to Jamaica, it relocated to temporary quarters on the campus of Queensborough Community College, also in Bayside. In September 1971, after holding classes at Queensborough for three academic years, the College moved into a combination of rented and purchased properties in Jamaica. At the same time, Milton G. Bassin began his twenty-year tenure as president. Over the next decade, the College underwent expansive curricular development. While a liberal arts emphasis was maintained, career-related majors in the health professions and business were also instituted. The Office of Continuing Education opened and began addressing the needs of the Jamaica community. In the mid-seventies, New York City's fiscal crisis placed a veil of uncertainty over York's future. In May of 1978, however, the Board of Higher Education assured the permanence of York College, issuing a resolution which affirmed its construction and mandated its development as a center for the health and business professions in a cooperative education mode, in addition to the liberal arts.

In 1980, Governor Hugh Carey approved the construction of the core campus, participating in the ground breaking ceremony in December of that year. In September of 1986, the College held its first classes in its Academic Core. At that time the student enrollment was 4,276, the number of faculty was 173 and the College offered 43 bachelor of arts and bachelor of science programs. In September of 1990 the Performing Arts Center and Health and Physical Education facilities were opened, followed a year later by the athletic fields.