During the Barbary Wars, he served aboard Enterprise and accompanied Stephen Decatur into the harbor at Tripoli on 16 February 1804, as Decatur and his men burned the captured American frigate Philadelphia to prevent Tripoli from using her in battle. In the ensuing skirmish, an American seaman positioned himself between Decatur and an enemy blade. This act of bravery was attributed to Reuben James and to Daniel Frazier. For the rest of the war, James continued to serve Decatur aboard Constitution and Congress. During the War of 1812, he served in United States, under Decatur, and in President. On 15 January 1815, however, President was defeated by the British and James was taken prisoner.
After the war, he resumed service with Decatur, aboard Guerriere, and participated in the capture of the 46-gun Algerian flagship Mashouda on 17 June 1815. After peace was made with the Barbary states, James continued his service in the Navy until declining health brought about his retirement in January 1836.
He died on 3 December 1838 at the US Naval Hospital in Washington, D.C.