Established to give relief to sick poor non-Friends, the New York Female Association first provided aid to sufferers of Yellow Fever. In 1800, following a proposal to open free schools for poor children who lacked other means of obtaining an education, the NYFA opened New York's first public school for female students; Theresa Garvan was employed as the teacher. Until 1845, when it turned its school interests entirely over to the Free School Society, established in 1805 by Quaker men, the NYFA worked in conjunction with the FSS, and by 1825, 750 girls were attending several schools and learning reading, writing, arithmetic, and needle-work. Three years later, however, the schools for girls were dropped due to under-enrollment and the students began attending FSS coeducational schools. The same year, the Association opened a new infant school in the basement a Lutheran church, which it ran until 1845. That year, the association turned over its school affairs entirely to the FSS and since has contented itself with small gifts to public and private charities. In 1853, the Government of the City of New York assumed full responsibility for the educational system.

In 1915, the New York Female Association commissioned the Lindley Murray Fund, a charity organization formed to provide aid to black and native Americans, to manage its funds. It continues as of 1988 as a gift- giving committee consisting of six Quaker members. Although the association has never been affiliated strictly with either the Hicksite or Orthodox meetings, in 1828, the committee was primarily if not entirely Orthodox, and by 1901 the organization was composed entirely of Hicksites.