After his return to the United States in 1885, he was for two years professor of music in the Cathedral School of St. Paul in Garden City, Long Island. From 1888 to 1893, he was organist of Trinity Church, New York City, and from 1893 to 1901 organist of Trinity Church, Boston. In 1893, Parker became Battell Professor of the theory of music at Yale University. He was appointed Dean of Music at that school in 1904, a position which he held for the rest of his life.