In 1861, Gibbon was stationed at Fort Leavenworth, Kansas, as the captain of the 4th US Artillery. Remaining with the Union army, he was promoted to brigadier general in May 1862. He first participated in combat at the Second Battle of Manassas. In September, his brigade participated in the battles of South Mountain and Antietam. He was promoted to division commander during the Battle of Fredericksburg. He later served at the battle of Chancellorsville, and at the Battle of Gettysburg. After Gettysburg, he waited for the promotion that did not come, participating in the battles of Wilderness, Spotsylvania Courthouse, and Cold Harbor. He was finally promoted to major general in June 1864, when he left the Army of the Potomac to command the XXIV corps of the Army of the James. In this command, he participated in the siege of Petersburg, and the Appomattox campaign. He continued to serve in the army after the end of the war.