John Joseph McGee (August 6, 1845 – April 10, 1927) was Clerk of the Privy Council of Canada from May 20, 1882 to May 5, 1907 and is the longest-serving occupant of the position.
Born in Wexford, Ireland, McGee immigrated to Canada in 1863 at the request of his half-brother D'Arcy McGee.
He finished his education at McGill University and joined the civil service in 1879 as a first class clerk in the Department of the Interior.
He became Assistant Clerk of the Queen's Privy Council in 1880 and became Clerk of the Privy Council two years later.