John Thomas McDonough (b. July 12, 1843 Birdhill, County Tipperary, Ireland – d. March 21, 1917 Washington D.C.) was an American lawyer and politician.

In 1891, he ran in the Third Judicial District for Justice of the New York Supreme Court, but was defeated by Democrat D. Cady Herrick.

In 1896, he was appointed by Governor Levi P. Morton New York State Commissioner of Statistics of Labor.

From June 17, 1903, to May 1, 1904, appointed by President Theodore Roosevelt, he was an Associate Justice of the Supreme Court of the Philippines.

In 1907, he ran on the Independence League ticket for the New York Court of Appeals but was defeated.