Lieutenant Commander Semmes joined the U.S. Navy as a midshipman in October 1841. He quickly rose through the ranks until he earned the rank of Lieutenant Commander on July 16, 1862 during the American Civil War. He served in command of U.S. gunboat Tahoma, U.S.S. Wamsutta, and Portsmouth. From August 1864 until March 1865, he commanded a ironclad named the U.S.S. Lehigh. His cousin, Raphael Semmes won renown as the commander of the CSS Alabama.