Harrison began his political career when he resigned from the military on June 1, 1798 and campaigned among his friends and family for a post in the Northwest Territorial government. His close friend Timothy Pickering was serving as Secretary of State, and he helped him to get a recommendation to replace Winthrop Sargent, the outgoing territorial secretary. President John Adams appointed Harrison to the position in July 1798. He also frequently served as acting territorial governor during the absences of Governor Arthur St. Clair.