In Wheeling, Lee met and married Sarah Ann Row. Reverend Robert E. L. Strider, Sr., who later became the Bishop of the West Virginia, conducted the ceremony at St. Matthew's Church in Wheeling on 24 September 1917. The couple's only child, John Clifford Hodges Lee, Jr., was born on 12 July 1918 and would likewise become a career Army officer, serving in World War II and various domestic assignments, ending his career as Colonel leading the Office of Appalachian Studies, and dying in 1975.