During the American Revolutionary War, Mercer was commissioned a captain in the 3rd Virginia Regiment in the Continental Army. He was wounded at the Battle of Brandywine. In 1778 he became an aide-de-camp with the rank of major to General Charles Lee. He resigned from the army when Lee did, but reentered the war as a lieutenant colonel in the Virginia militia. He served briefly under Lafayette in Virginia and was present at the siege of Yorktown. He was the brother of George Mercer and James Mercer.