Ellis was a member of the New Hampshire House of Representatives in 1803. He was elected as a Federalist to the Ninth Congress (March 4, 1805 – March 3, 1807). After service in Congress, he was member of the New Hampshire Governor’s council 1809 and 1810. In addition, he served in the New Hampshire Senate in 1811. He was a presidential elector on the Clinton and Ingersoll ticket in 1812. He was appointed judge of the superior court of New Hampshire in 1813, which office he held until his death in Claremont, New Hampshire in 1816. He was buried in Broad Street Cemetery.