Two months before his 29th birthday, J. Wallace Scott became one of Pennsylvania's early responders to President Abraham Lincoln's call for volunteers to defend Washington, D.C. following the April 1861 fall of Fort Sumter to the Confederate States Army. After enrolling for military service in West Chester on June 4, 1861, he mustered in as a private with Company A of the 1st Pennsylvania Reserve Regiment (also known as the 30th Pennsylvania Volunteer Infantry). Promoted to the rank of corporal early during his tenure of service, he and his men captured two enemy supply wagons while assigned to picket duties along an Annapolis Railroad line in Virginia in August 1861. Drawn by two horses each, the wagons were loaded with $5,000 worth of gold bullion and silk slated for use in CSA military uniforms and flags, as well as quinine supplies destined for CSA physicians. Engaged with his regiment in the Seven Days Battles near Richmond, Virginia from June 25 to July 1, 1862, including the battles of Beaver Dam Creek (June 26), Gaines's Mill (June 27), Savage's Station (June 29), Glendale (June 30), and Malvern Hill (July 1), he then fought in the Second Battle of Bull Run (August 28–30), and the battles of South Mountain (September 14) and Antietam (September 17). Advanced to the rank of sergeant, he was honorably discharged on October 23 in order to assume a new post with a different regiment.