Gibson entered service July 31, 1861, and by August 31 was named Colonel of the Forty-Ninth Regiment, Ohio Volunteer Infantry. Gibson was the 49th Ohio Infantry's commanding officer throughout the U.S. Civil War. In August and September 1861, he organized and trained the 49th Ohio Infantry at Camp Noble, near his home in Tiffin, Ohio. With Gibson in command, the regiment was mustered for three years and fought at 42 Civil War battles including: the Battle of Shiloh, the Siege of Corinth, the Battle of Stone River, the Tullahoma Campaign, the Battle of Chickamauga, the Battle of Missionary Ridge, the Atlanta Campaign, the Battle of Resaca, the Battle of Kennesaw Mountain, the Siege of Atlanta, the Battle of Jonesboro, the Second Battle of Franklin, and the Battle of Nashville.