In 1862, Badeau joined the Union Army during the American Civil War and was commissioned as a captain. As a member of the staff of Thomas W. Sherman, he took part in the Siege of Corinth, Mississippi, the defense of New Orleans, and the Siege of Port Hudson. where he was severely wounded. After his recovery, in March 1864, on the personal recommendation of Grant's adjutant, General John A. Rawlins, Badeau joined the staff of Ulysses S. Grant as a brevet lieutenant colonel and military secretary. During this time Badeau and Grant became close friends. Badeau took part in the Wilderness and Appomattox campaigns, and received promotion to brevet colonel. He remained on Grant's staff until 1869, and left the Army for disability caused by his Port Hudson wound; he held the permanent rank of captain and the brevet rank of brigadier general.