During the American Civil War, Marye volunteered for the Confederate army shortly after Virginia's secession, first serving as a private in Pollock's Company (a/k/a Fredericksburg Light Artillery), whose commanders were Carter Braxton and Edward A. Marye (1835-1864). Despite his relatively advanced age, J.L. Marye Jr. rose to the rank of sergeant before his discharge. Although this light artillery company was originally designated to protect its local area (Aquia and Stafford north of Fredericksburg), it began to see more action in the Battle of Williamsburg in May 1862. By mid-1862, Fredericksburg itself became contested, and the Washington Artillery of New Orleans quartered on the Marye estate in Fredericksburg (Brompton) during the fierce fighting in the Battle of Fredericksburg in mid-December 1862, although it was captured during the Second Battle of Fredericksburg so that the next year it would become a hospital for injured Union soldiers.