After studying law for a time, Woolsey entered the Navy as a midshipman on April 9, 1800. His first assignment was the frigate , on which he made a cruise to the West Indies in 1800 and 1801. He served briefly in the First Barbary War just before its end in 1805. In 1807, the newly promoted Woolsey received orders to Washington, D.C., where he developed a code of signals for the Navy.