During the American Civil War, Craig served as a brigadier general of U.S. volunteers. From April to November 1862, Craig was the military commander in charge of the overland mail routes in Kansas and Nebraska. On November 2, 1862 he assumed command of the District of Nebraska Territory and commanded until May 5, 1863 when he resigned. Craig again served as a brigadier general, this time in the Missouri State militia, in 1864 and 1865. He is buried in Mount Mora Cemetery.