Promoted to captain in 1846, Chilton fought in the Mexican-American War, winning the brevet rank of major for gallantry in the action at the Battle of Buena Vista. Under severe Mexican fire, he picked up the wounded Colonel Jefferson Davis and carried him to safety. He was assigned to administrative duty as a paymaster with the rank of major in 1854; serving in various posts in Washington, D.C., New York City, Detroit, Michigan and San Antonio, Texas.
Chilton was in Texas when he received word of the bombardment of Fort Sumter. He resigned his commission in the U.S. Army on April 29, 1861, and traveled home to Virginia. He enrolled in the Confederate service as an adjutant general with the rank of lieutenant colonel. He served on the staff of fellow Virginian, Robert E. Lee, rising to chief of staff. He did not pen the famous Lost Order during the Maryland Campaign. The identity of the writer of the Lost Order that McClellan received from the field is yet to be identified. (See “Special Order 191-Ruse of War”) Although nominated for brigadier general in October 1862 and despite firm support from General Lee, Chilton's appointment was not officially confirmed by the Confederate Congress until February 16, 1864, most likely due to repeated clashes with the Confederate Senate and with fellow officers, most notably John B. Magruder.
Following the Gettysburg Campaign, he served as Inspector General for the Army of Northern Virginia for the rest of the war, with his headquarters in Richmond, Virginia. He rarely led troops in the field, with the exception of a successful attack in May 1864 when he led a small force of Virginia troops in routing Federal troops from the Army of the James that were raiding the important Richmond & Petersburg Railroad.
Following the cessation of hostilities in early 1865, Chilton returned to civilian life. He moved to Columbus, Georgia, where he became president of a local manufacturing company. He died of apoplexy in Columbus in 1879. He is buried in Hollywood Cemetery in Richmond, Virginia.