He recruited Company E, Second Kansas Volunteer Infantry, from Anderson and Franklin Counties for duty with the Union Army. Later he commanded elements of the Second Kansas Cavalry and the 83rd U.S. Colored Infantry, where he gained recognition as a heroic military leader during the Civil War.

He was sworn in as the third Kansas Governor on January 9, 1865 and was reelected for a second term two years later. Due to his concern for Western Kansas settlers who were suffering violent raids by hostile plains Indian tribes, Governor Crawford issued a call for volunteers to serve a period of six months.

He resigned as Governor on November 4, 1868 to take command of the 19th Kansas Volunteer Cavalry Regiment which was to join the 7th U.S. Cavalry in the Custer-Sheridan winter Campaign of 1868-69. The purpose of their operation was to force the Indians into their reservations and to demonstrate that the winter offered no sanctuary for the plains tribes. Heavy precipitations, sub-freezing temperatures, a severe shortage of rations for the soldiers and forage for their horses combined to create great suffering for the men and their animals during the entire winter. Col. Crawford's distinctive leadership sustained the Kansas Volunteers, proving that the U.S. Army could and would operate in any weather.