St. Philip's Church traces its origins back to 1704, when Elias Neau taught enslaved New Yorkers to read the Bible.

St. Philip's Episcopal Church separated from New York's Trinity Episcopal Church and formed a separate congregation, under the leadership of Peter Williams Jr., a graduate of the African Free School. Its congregation eventually grew frustrated with segregation and formed the Free African Church of St. Philip. The church became a hub for abolitionist activity and mutual aid, enduring multiple attacks, including the 1834 riot and the Civil War Draft Riots.

Despite these challenges, it thrived and relocated to Harlem in 1910, continuing its dedication to worship and social justice. St. Philip's was designed by Vertner Woodson Tandy, New York State's first black registered architect.