At the start of the Civil War, Captain French and the 1st U.S. Artillery were stationed at Fort Duncan, Eagle Pass, Texas. He refused to surrender his garrison to the Confederate-aligned state authorities as they requested. Instead, he moved his men to the mouth of the Río Grande in sixteen days and sailed to Key West, where he quartered at the Federal military post there, Fort Zachary Taylor. Shortly thereafter, he was elevated to major and assumed command of the base. In conjunction with the Union Navy, he was instrumental in shutting off Key West to slave traders. He was promoted to brigadier general of volunteers as of September 28, 1861, and was assigned to the Army of the Potomac, where he commanded a brigade of the II Corps in the Peninsula Campaign. He was engaged at the battles of Yorktown, Seven Pines, Oak Grove, Gaines' Mill, Garnett's & Golding's Farm, Savage's Station, Glendale, and Malvern Hill. French received praise in official reports for his actions and leadership, and was promoted to command a division during the Northern Virginia Campaign. French commanded the 3rd Division of the II Corps at the Battle of Antietam, making the first attack on Confederate units in the Sunken Road. He was promoted to major general on November 29, 1862. He led his division in the battles of Fredericksburg and Chancellorsville. French commanded elements of the VIII Corps and the District of Harpers Ferry during the Gettysburg Campaign, but shortly after Maj. Gen. Daniel E. Sickles was wounded at the Battle of Gettysburg, French assumed command of the battered III Corps. His military reputation was ruined during the Mine Run Campaign in November 1863 when Maj. Gen. George G. Meade claimed that French's corps moved too slowly to exploit a potential advantage over Gen. Robert E. Lee. This engagement was the last for the III Corps, which was reorganized out of the Union Army in the spring of 1864, and French was mustered out of volunteer service on May 6, 1864. He remained in the regular army, and for the remainder of the war, he served on military boards in Washington, D.C. French ended the war with the regular army rank of colonel of the 4th U.S. Artillery.
Postbellum career
Following the war, French commanded the 2nd Artillery on the Pacific Coast from 1865 until 1872, including an assignment as commander of Fort McDowell in San Francisco Bay. In 1875, he was appointed the commander of Fort McHenry near Baltimore. In July 1880, at his own request, being over sixty-two years of age, he was retired. French died in Washington, D.C., and is buried there in Rock Creek Cemetery.
Family
He married Caroline Read. They had six children: Frank French, William H. French, Anna French Clem, Frederick French, George French, and Rosalie French Conklin. His grandson, John French Conklin, was also a graduate of the U.S. Military Academy and a brigadier general in the United States Army.