The Confederate forces at the Battle of Antietam were commanded by General Robert E. Lee.

He led the Army of Northern Virginia into Maryland with the aim of securing a victory on Union soil, which he hoped would sway public opinion in favor of the Confederacy and potentially lead to foreign recognition. Lee’s strategic prowess was on display during the battle, as he skillfully positioned his troops against Union forces. Despite facing a larger enemy, Lee’s leadership resulted in a fierce and bloody confrontation, solidifying his reputation as one of the war's most formidable commanders.