In 1837, Draper accepted an appointment to be head of chemistry in a proposed medical school at New York University, but sufficient funds were not available to go ahead with the project. In 1839, Draper was elected undergraduate professor of chemistry and botany at the university, and moved with his family to New York City . Once there he helped to found the New York University Medical School, acting as a professor there from 1840 to 1850, president of the school from 1850 to 1873, and as a professor of chemistry until 1881.