In 1861, French was in service in command of a garrison in Texas. When ordered to the east, he refused to surrender his garrison to the state. He led his troops to the federal post at Key West, Florida. On September 28, 1861, he was appointed a brigadier general of volunteers, and commanded a brigade in the II Corps of the Army of the Potomac in the Peninsula Campaign and Seven Days' Campaign. At the Battle of Antietam, French led a division, and afterward, he was promoted to major general on November 29, 1862. He would serve at the Battle of Fredericksburg, and at the Battle of Chancellorsville. In July 1863, French commanded the Union forces in the Battle of Manassas Gap during the pursuit of the Confederate army after the Battle of Gettysburg. Subsequently, in October 1863, he led the Union forces involved at the Battle of Auburn, during the Bristoe campaign. This move earned him a temporary promotion to the command of the III corps during the Mine Run campaign, a position which he soon lost after he delayed operations and contributed to the failure of this campaign. Subsequently, he was relieved of command in May 1864, and served on military boards.