At the outbreak of the war, Hebert joined the Confederate army as colonel of the 3rd Louisiana Infantry. He served at the battle of Wilson's Creek, Missouri, before he was captured at the Battle of Pea Ridge. After his exchange, he was promoted to brigadier general. He was appointed to northern Mississippi, participating in the battles of Iuka, Corinth and in the siege of Vicksburg. Hebert assumed command of the artillery in the Battle for Fort Fisher, and acted as chief engineer of North Carolina until the end of the war.