In 1862, at the age of seventeen, Estopinal left school to enlist as a soldier in the St. Bernard Guards of the 28th Louisiana Regiment of the Confederate Army. He began as an orderly sergeant in Company G. He fought in the Battle of Chickasaw Bayou in December 1862, the opening exchange of what became in July 1863 the decisive Battle of Vicksburg, Mississippi, in which he commanded a squad which transported prisoners from Indianola in Sunflower County in northwestern Mississippi, to Libby on the Gulf Coast.