The Episcopal School opened on October 25, 1961 in borrowed space with an enrollment of thirty-five children. In January 1962, the School moved into two classrooms leased from the Church of the Resurrection. In the fall of that year, two additional classrooms were leased and the enrollment grew to seventy children.

In 1966, The Episcopal School was chartered by the Board of Regents of the State of New York. The School purchased its current town house at 35 East 69th Street in 1972. Renovations were completed and the building opened in September 1974. In 1986, the fifth and sixth floors were added.

Until the 1994-95 school year, the School offered two-day and three-day sessions for toddlers. Believing that continuity benefits even Episcopal's youngest children, the School revised the program to accommodate two five-day, toddler-age groups.

By 1995, all ongoing schools in the city had established kindergartens. Soon thereafter, Episcopal's kindergarten program closed.

Currently, there are 200 children ages 2 years and 5 months to 5 years old attending either morning or afternoon sessions.