The meeting place of the Methodist Episcopal Church is known to have been a dwelling located on Greenleaf Point, South Capitol and N Streets, Washington, D. C. in 1805. The membership consisted of sixty-one white and twenty-five black members. They moved to Dudley Carroll's barn on New Jersey Avenue, south of D Street, S.E. in 1807. In 1811 another move was made to a newly constructed church at Fourth Street, S.E. between South Carolina Avenue and G Street. This was the first church built by Methodists in Washington and was named the Fourth Street Station.

In 1837, the black membership had outgrown the galleries which were reserved for them in the Mother Church. With the help and guidance of the Mother Church a lot was located at the corner of Fourth and D Street, S.E. and purchased on April 27, 1838. A small frame church building was immediately erected under the supervision of the pastor of the Mother Church assisted by three local preachers. The church was named Little Ebenezer.

The first black trustees, Alfred H. Perry, William Brown, Sr., William Brown, Jr., Benjamin Grant, Nathaniel Jackson, John Payne, James Hill, William Thomas and Noah Jones were appointed on October 18, 1860. The first black pastor, Rev. Noah Jones, was appointed in 1864. A choir was organized in the late 1860s to supplement the congregational singing which was the only form of musical worship at the time. Mr. William G. Miller, who had the idea to establish the choir, was appointed the first director.

After the start of the Civil War large numbers of black refugees from the South migrated to the District of Columbia. Between 1860 and 1863 the local black population increased by over two thirds; an increase which could not be ignored. The New England Freedmen's Aid Society of Boston responded by sending a teacher, Miss Frances W. Perkins. Miss Emma V. Brown, a prominent African-American, was later employed by the District Government to teach and on March 1, 1864 the first public, government-sponsored school for black children in Washington, D.C. was established and housed at Ebenezer.

In 1870, because of its progress and growth in the religious and civic actitivies in the southeast of Washington, D. C. the term `Little' was dropped from the church name and the church became known as Ebenezer Methodist Episcopal Church. Ebenezer was incorporated on September 28, 1891.

The present church structure was dedicated on November 4, 1897. It was designated a Historical Landmark on April 29, 1975.