The Chinese Independent Baptist Church San Francisco was established in 1905 when a group of believers worshiping at the First Chinese Baptist Church organized themselves into a separate church. This group of believers, led by the Rev. Tsai Leong Lee, had their roots in an indigenous Chinese Baptist movement in Guangzhou, China in the 1800’s.  It placed great emphasis on a unique approach to church life and church polity of “Self Governing, Self Propagating, and Self Supporting”, a missiological concept which was ahead of its time. The church actually created history of sorts. It became the first Chinese church to be organized after the passage of the Chinese Exclusion Act of 1882. It was also the first Chinese church in San Francisco (and one of the first in the nation) that was established by indigenous Chinese Christians. They met in rented quarters on Clay Street.

In 1906, the Great Earthquake struck San Francisco.  Their meeting place was destroyed and part of the congregation moved to Oakland to live while some of the members remained in San Francisco. After the Quake, the church continued meeting in two locations. The San Francisco group bought property in 1913 on Washington Street and the building was completed in 1922. The Oakland group bought property in 1963 and built on their present location on 8th Street. In 1967, the San Francisco and the Oakland congregations became two autonomous churches – Chinese Independent Baptist Church San Francisco and Chinese Independent Baptist Church Oakland.

In 1975, the San Francisco church established a missions point in the Sunset District which later became the Sunset Chinese Baptist Church in 1980 (presently Sunset Church of San Francisco). In 1976, the Marin County mission point was established and it later became the Marin Community Church.

Since the seventies, the church began supporting missionaries serving in the mission field and mission organizations funding these with money above and beyond what the members normally give to the church. Since the late eighties, it began sending out short-term missionaries to Belize, China, Costa Rica, Macau, Malaysia, Mexico, Myanmar, and Arizona, USA.

In 1985, it joined with several other Chinese Baptist churches in the San Francisco Bay Area to form the Northern California Chinese Baptist Association. It is also a member of the Chinese Christian Union of San Francisco and the Chinese Baptist Fellowship of the US and Canada.

In 2003, the church affirmed its commitment to remain in San Francisco Chinatown by pledging its resources to build a four story addition and do a major renovation of the existing church building. This was later reaffirmed in 2007 with the launch of Operation Future Hope which sought to use the building program to not only build and improve a facility that would glorify God but also building a people after God’s heart. By the grace and mercy of God, the $2.4 million project was completed debt-free and the new building, aptly called the “Faith Building”, dedicated to the Glory of God on April 3 2010.  With the new and added facilities, the church would be able to expand its ministry of preaching the Gospel of Jesus Christ in word and in deed to the community and helping it to realize its mission to “Know Christ and to Make Him Known beginning in San Francisco Chinatown.”