He served as chief of staff for the Army of Northern Virginia under Robert E. Lee for much of the war.

The couple had three children: Laura Mason, Emily Virginia, and Robert Lee Chilton.

Promoted to captain in 1846, Chilton fought in the Mexican–American War, winning the brevet rank of major for gallantry in 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.

The second occurrence where Col. Chilton placed the Army of Northern Virginia in a position of potential destruction was during the Chancellorsville campaign.

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 because of repeated clashes with the Confederate Senate and with fellow officers, most notably John B. Magruder.