John Thompson (March 20, 1749 - died 1823) was a United States Representative from New York. Born in Litchfield, Connecticut, he attended the common schools, and at the age of fourteen moved with his parents to Stillwater, New York. He was appointed justice of Stillwater Township in 1788 and was a member of the New York Assembly in 1788 and 1789. Thompson was elected as a Democratic-Republican to the Sixth Congress, serving from March 4, 1799 to March 3, 1801. He was a delegate to the New York State Constitutional Convention in 1801, and was appointed by Governor George Clinton in 1791 as the first judge of Saratoga County, holding this office until 1809. Thompson was then elected to the Tenth and Eleventh Congresses, serving from March 4, 1807 to March 3, 1811. He died in 1823 and was interred at Stillwater.