Born in St. Louis, Missouri, Paul was the grandson of René Auguste Chouteau. He graduated in 1834 from the United States Military Academy, 18th of 36 cadets in his class. He served as an officer in the 7th U.S. Infantry during the Seminole Wars and the Mexican–American War. He was wounded at the Battle of Cerro Gordo, but recovered to serve in the campaign to capture Mexico City. He led an assault party that captured a Mexican flag during the storming of Chapultepec.