Rock County Christian School was started by a group of pastors who worked together in the Rock County Evangelical Ministerial Association in 1985. The school was called Janesville Christian School until 1990.

In the fall of 1985, Janesville Christian School started with grades K-6. One grade per year was added until the school grew to K-9th grade in the 1988-1989 school year. For this period of time, classes were conducted in a school building which had been purchased from the Janesville school district. This building is located halfway between Janesville and Beloit Wisconsin.

In 1990, the school expanded to K-12. This expansion was accomplished through the purchase of a second building in Beloit, Wisconsin, from a church that operated a small Christian school. It was at this time that the school changed its name to Rock County Christian School. The first graduating class of RCCS was the class of 1991.

In the fall of 1998, a preschool program was implemented at the Janesville Campus. In 2008, an infant care program was initiated in the house on the property adjacent to the Janesville Campus. Both of these programs were discontinued in the spring of 2015.

At the present time, grades K-5 attend classes at the original Janesville Campus and grades 6-12 attend classes at the Beloit Campus. The school’s enrollment has fluctuated from around 150-275 students.

In 2013, Rock County Christian School became the first WPCP (Wisconsin Parental Choice Program) school in Rock County and received 28 vouchers for CHOICE students. Eleven of those CHOICE students were previously attending RCCS and 17 were new enrollees. When the cap to the CHOICE program was revised the summer of 2015 to allow 1% of each school district, many RCCS families that have sacrificed financially and/or received scholarships were able to benefit from their own tax dollars supporting their choice of RCCS.

In 2016, RCCS became accredited through Wisconsin Religious and Independent Schools Accreditation (WRISA).

In 2017, a new full-size gym was built at the Beloit Campus.