In 1912, Stoddard enlisted in the Veteran Corps of Artillery. During the 1916 Mexican Expedition, he entered the U.S. Army and served on the Mexican border as battalion adjutant in the 71st Infantry, U.S. National Guard. In 1917, when America entered World War I, he was commissioned major in the Coast Artillery Corps of the New York Guard. He was then sent abroad as the ranking member of a commission to study anti-aircraft artillery methods of the 3rd British Army on the Somme front and the 10th French Army on the Aisne front. In 1918, he was commissioned Major of Ordinance. After graduating from the Army War College, he served as Division Ordinance Officer of the 17th Division until his discharge in January 1919. Later that year, he was commissioned Lieutenant-Colonel Ordinance of the Officers Reserve Corps and appointed Division Ordinance Officer of the 98th Division of the organized reserves. From 1923 to 1935, he was a colonel commanding the 53rd Coast Artillery. He retired as a colonel in the Army Reserves. He was also military aide to Mayor La Guardia during World War II and organized the New York City Patrol Corps.