Wilkinson first served in Thompson's Pennsylvania rifle battalion, 1775–76, and was commissioned a captain in September 1775. He served as an aide to Nathanael Greene during the Siege of Boston, participated in the placing of guns on the Dorchester Heights in March 1776, and following the British abandonment of Boston, went with the rest of the Continental Army to New York where he left Greene's staff and was given command of an infantry company.