Dr. McGuire joined "The Winchester Rifles," Company F of the 2nd Virginia Infantry as a private in the Confederate Army. However, his services were much more valuable as a doctor rather than a front line soldier. McGuire was made a brigade surgeon and was ordered to report to General Thomas J. Jackson at Harpers Ferry. Jackson initially scoffed at McGuire's youth, but the two became very close as the war progressed. Dr. McGuire treated General Jackson after the First Battle of Manassas, where the General picked up the nickname "Stonewall Jackson" following an exclamation by General Barnard E. Bee Jr. (who himself was killed during the battle).