When the Civil War broke out in April 1861, Hickok signed on as a teamster for the Union Army in Sedalia, Missouri, and by the end of the year he was a wagonmaster. In September 1862 he was discharged for an undisclosed reason and there are no records of his whereabouts until late 1863, when he was employed by the Provost Marshal of South-West Missouri as a member of the Springfield detective police. It has been speculated that during the "missing year", Hickok may have been operating as a spy in Southern territory.
Hickok's duties as a police detective were mostly mundane and included counting the number of troops in uniform drinking while on duty, checking hotel liquor licenses and tracking down individuals in debt to the Union to facilitate repayment. In 1864 Hickok and the other detectives had not been paid for some time, and Hickok either resigned or was reassigned as he was hired as a scout by General John B. Sanborn at five dollars a day plus a horse and equipment. In June 1865, Hickok was mustered out and spent his time in and around Springfield gambling.