In October 1869, twelve people were dismissed from the fellowship of the First Baptist Church of Manhattan, Kansas for the purpose of organizing a Baptist Church in Clay Center. At the time, Clay Center was only a village of around 100 people.  Later, on February 26, 1872, a Charter was filed with the Secretary of State of Kansas, thus making the First Baptist Church the first church to be organized in Clay Center, Kansas.

Over the next two years,  a stone church building was completed and dedicated in 1874 with a membership of 35. The Methodist, Presbyterian and other denominations also used the church while the Baptists conducted a combined Sunday School.

By 1881, the membership has grown to 75. Three years later the church debt had been paid and the church repaired, painted, an Estay organ was purchased and installed, and the grounds put in order and fenced. During this time, a parsonage was also built and church attendance had reached almost 220.

The vision for the current sanctuary began with the coming of Rev. J.W. Bayles on June 3, 1909. That fall, a committee was appointed to plan for the present church. They estimated the cost at $15,000.  On April 22, 1910, an "old time social" was held as a farewell to the old stone church building. Nearly 300 people regularly attended First Baptist Church at that time.

On April 20, 1911 - one year after the old church had been torn down - the new church building was dedicated to the "cause of God". At that service, eight members pledge to fund the remaining balance on the building. The total cost for the building was nearly $25,000.  When completed, the church was known as the "handsomest house of worship in this part of Kansas".

Between 1920 and 1922, under the pastorate of W.W. Carpenter, the church joined other community churches in hosting a successful revival and as a result many new members were added to the various churches.

On April 30, 1936, during a celebration of the Twenty-fifth Anniversary of the completion of the new church, a deed to the lots east of the church were presented by Mrs. Eric H. Swenson as a memorial to her late husband. On this property, an education unit was added and it was dedicated on November 3, 1963.

On November 10, 2002, a new addition featuring classrooms, offices and fellowship hall were dedicated and is now enjoyed by all. God truly has blessed this church and we are thankful for the guidance and gifts that He has provided.

The church has had 27 pastors in its history. Recent pastorates include Rev. Don Gaines serving 23 years, Rev. Dan Kline serving 13 years, Rev. Brian High serving from 1.5 years. Pastor Matthew Coleman and his family began serving the congregation on August 2, 2010. 

The congregation celebrates the 140th Anniversary of the incorporation
of First Baptist Church of Clay Center, KS.

Most recently, during the summer of 2017, the congregation of First Baptist Church of Clay Center, KS voted to dissolve its affiliation with the American Baptist Churches of the United States of America (ABCUSA) as well as the American Baptist Churches of the Central Region (ABCCR).  The congregation is currently unaffiliated with any denomination.