Allen served as a member of the Vermont House of Representatives from 1812 until 1817. While in the State House he received the appointment of quartermaster of militia, with the rank of Brigadier general. He was elected as a Democratic-Republican candidate to the Fifteenth Congress, serving from March 4, 1817 until his resignation on April 20, 1818. Allen resigned from Congress to become United States Marshal for the district of Vermont on December 14, 1818; he was reappointed on December 24, 1822. Allen was the agent for paying pensioners in 1819.