In its early years the congregation was part of the African Union Meeting and Schoolhouse.

The congregation was established in 1819 and originally met in a building located near the present site, the land having been given to them by Moses Brown.

The church is set into a hill, exposing a full brick basement, through which entrance to the building is gained.

In December 1968, 65 Black students from Brown University marched down College Hill to the Congdon Street Baptist Church.

They remained in the church for three days,[4] as a protest of the small number of Black students admitted to the University as well as a lack of institutional support.