In 1861, Torbert refused a commission in the Confederate Army. Remaining a lieutenant in the U.S. Army, he served as a regimental commander and then received the rank of brigadier general in 1862. He served at the First Battle of Manassas and the 1862 Peninsula Campaign, in which he saw action at Yorktown and Seven Days. He led forces at the Second Battle of Manassas and was wounded at South Mountain. Torbert later returned to fight at Antietam, Fredericksburg, Gettysburg, Bristoe Station, Mine Run, and throughout the Overland Campaign of 1864. He was eventually appointed as Commander of Cavalry in the Army of Shenandoah in 1864 and mustered out of the army in 1866.
