With the outbreak of the American Revolution, Harmar joined the army as a major in 1776. He served under Gen. George Washington and later under Gen. Henry Lee in the South. After its ratification by Congress, Harmar carried the treaty of peace to France.

After the war, Congress directed Harmar's federal troops to expel settlers and quell raids by Native Americans north of the Ohio River, in the Northwest Territory. In 1790, he pursued the Shawnee along the Scioto River. Moving north from Cincinnati, his units marched toward the Maumee valley, destroying villages and crops. Encountering resistance from a confederation of tribes under the leadership of Michikinikwa (Little Turtle), Harmar's small detachment was defeated. A subsequently deployed larger force under Harmar fought the same Native Americans to a standstill, but could not claim victory in the battle or success in resolving the tense situation.

After leaving the army, Harmar served as adjutant-general of Pennsylvania until his death on Aug. 20, 1813.