In August 1861, Gibson received his commission as a colonel in 13th Louisiana Infantry. He led his command into action at the Battle of Shiloh and then the Kentucky campaign. Gibson participated in the Battle of Chickamauga before marching to Atlanta. For his participation in the Atlanta campaign, and the subsequent invasion of Tennessee, he received a promotion to brigadier general in January 1864. His final service was in the defense of Spanish Fort, in Mobile, Alabama.