In 1899, Stokes took the post of Secretary of Yale University, second in command to the university's president, and he also served as assistant rector of Saint Paul's Episcopal Church in New Haven, Connecticut, from 1900 to 1918. From 1924 to 1939, Stokes was resident canon at the
National Cathedral in Washington, D.C. During this time, he became involved in many social, cultural, and ecclesiastical causes, and guided the philanthropy of the
Phelps Stokes Fund (established in 1911) to improve the lives of African and American blacks. In 1936, he published a short biography of
Booker T. Washington, which was an expanded version of a sketch he had written for the
Dictionary of American Biography. Stokes saw all of his work as "fellowship in the gospel" (Philemon 1:5). ==Personal life==