Christian Fellowship Congregational Church is one of the oldest Congregational Churches in continuous operation in the City of San Diego. Founded as the Second Congregational Church, the church was organized on the second Sunday in November 1887, when the Rev. A. B. White, of Toledo, Ohio began to preach in the schoolhouse on Twenty-seventh street. On February 19, 1888, the church building at Twenty-sixth street and Kerney Avenue was dedicated, Rev. Dr. John Silcox preaching the sermon.
The Land & Town Company gave the lots and the members of the First Congregational Church contributed liberally to the building fund. Mr. White resigned the following August, and F. B. Perkins became the pastor. He remained two years and resigned in 1890. The Rev. George A. Hall was then the pastor until March 24, 1895. His successor was the Rev. R.T. Earl, who ministered until 1902, who was followed by the Rev. J. L. Pearson from 1902-1905 and the Rev. E.E.P. Abbott from 1905-1908. In 1905 the name of the church was changed to Logan Heights Congregational Church as the church found a permenant location in the Logan Heights community of San Diego.
The Rev. Stephen G. Emerson was called as Pastor from the Lake Avenue Congregational Church, serving from 1908-1914. It was during this period that the church member grew and the new edifice was errected and paid in full.
From 1915 to 1945 the following clergy served as Pastor:
- The Reverend F. C. Reid (1914 – 1917)
- The Reverend W. H. Harmaford (1918 – 1920)
- The Reverend Arthur Metcalf (1921 – 1926)
- The Reverend C. H. Baldwin (1927)
- The Reverend J. Frederick Saunders (1927 – 1930)
- The Reverend J. Dayton Auxill (1932 – 1940)
- The Reverend Alvin G. Rowe (1941 -1942)
- The Reverend Raymond E. Kinney (1943 – 1944)
The Rev. E. Lowell Cantrell was the pioneering voice that opened the door for the church to welcome and embrace its first African-American minister, as the community of Logan Heights began to shift and change racially in the mid 1940’s. At a Special meeting of the church in July of 1946 Rev. Cantrell called the church to embrace the idea becoming an interracial church or close its doors. He said, firmly, “if the church would vote to make this an interracial [church] and call a colored ministered as co-pastor it would grow into an active church.” When asked if the vote were not to be taken would he stay on as pastor, Rev. Cantrell flatly told the church “there was no prospect.” The church, without much debate, chose to test out this new identity and soon called one its newest members, the Rev. E. Major Shavers to serve as co-pastor the church in Logan Heights. The vision they co-pastors shared was a one that was modeled on a ministry developed in San Francisco by the Rev. Drs. Howard Thurman and Alfred Fisk. Although only in ministry for one year, Rev. Cantrell used his power and privilege at the risk of his status, vocation and young family to welcome a new interracial era of Christian unity and Christian fellowship among like-minded believers.
In 1950 the name of the church was changed to Christian Fellowship Congregational Community Church. In 1957 the congregation voted to join in membership with United Church of Christ, and in 1983 the name of the church was changed to Christian Fellowship Congregational Church of San Diego, United Church of Christ.
Since 1945 the following clergy have served as Pastor
- The Reverend E. Lowell Cantrell (1945 – 1946)
- The Reverend E. Major Shavers (1946 – 1963)
- The Reverend John Everett (Interim Pastor)
- The Reverend Adlai Mack (1978 – 1984)
- The Reverend Dr. James Hester Hargett (1986 – 1997, Pastor Emeritus)
- The Reverend Arthur L. Cribbs, Jr. (1999 – 2007)
- The Reverend Dr. Ameila Walker (Interim Pastor)
- The Reverend Dr. J. Lee Hill, Jr. (2010 – present)
 July 26, 1946, Church Minutes.