After the start of the Civil War, Hitchcock applied to return to the service, but was rejected. It was only after the intervention of Winfield Scott that he was commissioned a major general in February, 1862 and became special adviser to the Secretary of War. From March 17 to July 23, 1862, he served as the chairman of the War Board, the organization that assisted President Abraham Lincoln and Secretary of War Edwin M. Stanton in the management of the War Department and the command of the Union armies during the period in which there was no general-in-chief. (Maj. Gen. George B. McClellan had been relieved of his responsibilities as general-in-chief and Maj. Gen. Henry W. Halleck had not yet replaced him.)