In September 1961, the Fairfax Christian School opened its doors in Fairfax, Virginia. Its first location was on the ground floor of a large Victorian home. The school opened offering classes in kindergarten through eighth grade. A grade was added each year thereafter. The first high school student graduated in 1968. The Fairfax Christian School has offered classes in kindergarten through high school ever since.

By 1968, the student population had grown to over 650 students. In 1983, after selling the Popes Head Road campus, the school moved to several different churches while waiting approval from the county government to build a new campus. In 1992, the school moved into a campus located on Hunter Mill Road in Vienna, Virginia. 

The school outgrew their Vienna location and in 2018, the Fairfax Christian School moved to a new, larger campus in Dulles, Virginia.

In 1981, the school was featured in an article in People Magazine. A highlight of the article was that Fairfax Christian School was the school where many Washington area conservatives sent their children. Many Washington politicians and local celebrities and athletes have sent their children to Fairfax Christian School. Five Fairfax Christian School parents have run for President of the United States.

Noteworthy alumni include former US Senator Evan Bayh (Democrat – Indiana), US Congressman Robert Latta (Republican – Ohio), David Buckley – former Inspector General of the Central Intelligence Agency and acclaimed musicians Lee Cantelon and Paul Cantelon.