Eisenhart was the son of Luther Eisenhart, a prominent mathematician in his own right.
Churchill Eisenhart was brought to the NBS from the University of Wisconsin–Madison in 1946 by Edward Condon, Director of the NBS, to establish a statistical consulting group to "substitute sound mathematical analysis for costly experimentation." He was allowed to recruit his own staff and, over the years, he brought many notable and accomplished statisticians to SEL. He served as its Chief from 1947 until his appointment as Senior Research Fellow in 1963. He retired in 1983 after which he formed the Standards Alumni Association, which he headed until his death in 1994.