Edward Higgins entered the Confederate States Army on April 12, 1861, as a captain in the 1st Louisiana Artillery Regiment. On June 12, 1861, he became aide-de-camp to Major General David E. Twiggs. Higgins supervised the construction of the defenses of Ship Island. On October 29, 1861, he was appointed captain in the CSA 1st Artillery Regiment. Higgins resigned from this position on January 2, 1862, and on February 13, 1862, he was appointed lieutenant colonel of the 21st Louisiana Infantry Regiment. Higgins was captured on April 28, 1862, while defending Fort Jackson and Fort St. Philip during the Union Army's attack on and occupation of the lower Mississippi River and New Orleans, Louisiana. After a brief imprisonment, Higgins was exchanged on October 16, 1862.