He entered what became the Army of Northern Virginia in June 1861 as captain of the King William Artillery. His younger brother, Julian Carter of the 4th Virginia Cavalry, was killed in late July 1862 at a minor skirmish near Malvern Hill. Tom Carter was wounded in the foot at Sharpsburg. In December he was promoted to major, a rank he held until he became a lieutenant colonel in April 1863. By the Gettysburg Campaign of 1863, Carter commanded a battalion of artillery in Lt. Gen. Richard S. Ewell's Second Corps. His guns unlimbered on Oak Hill northwest of Gettysburg and contributed to the eventual withdrawal of the Union First Corps of the Army of the Potomac. Carter's guns later supported Pickett's Charge on July 3. Promoted to colonel in March 1864, he remained with the Army of Northern Virginia during the Overland Campaign until September when he left to temporarily replace Brig. Gen. Armistead L. Long as chief of artillery for Lt. Gen. Jubal A. Early during the second half of Early's Valley Campaigns of 1864. Carter fought in several important battles, including the Battle of Cedar Creek.