The action moved to the southern end of the battlefield. McClellan's plan called for Maj. Gen. Ambrose Burnside and the IX Corps to conduct a diversionary attack in support of Hooker's I Corps, hoping to draw Confederate attention away from the intended main attack in the north. However, Burnside was instructed to wait for explicit orders before launching his attack, and those orders did not reach him until 10 a.m.^[29] Burnside was strangely passive during preparations for the battle. He was disgruntled that McClellan had abandoned the previous arrangement of "wing" commanders reporting to him. Previously, Burnside had commanded a wing that included both the I and IX Corps and now he was responsible only for the IX Corps. Implicitly refusing to give up his higher authority, Burnside treated first Maj. Gen. Jesse L. Reno (killed at South Mountain) and then Brig. Gen. Jacob D. Cox of the Kanawha Division as the corps commander, funneling orders to the corps through him.

Burnside had four divisions (12,500 troops) and 50 guns east of Antietam Creek. Facing him was a force that had been greatly depleted by Lee's movement of units to bolster the Confederate left flank. At dawn, the divisions of Brig. Gens. David R. Jones and John G. Walker stood in defense, but by 10 a.m. all of Walker's men and Col. George T. Anderson's Georgia brigade had been removed. Jones had only about 3,000 men and 12 guns available to meet Burnside. Four thin brigades guarded the ridges near Sharpsburg, primarily a low plateau known as Cemetery Hill. The remaining 400 men—the 2nd and 20th Georgia regiments, under the command of Brig. Gen. Robert Toombs, with two artillery batteries—defended Rohrbach's Bridge, a three-span, 125-foot (38 m) stone structure that was the southernmost crossing of the Antietam.^[30] It would become known to history as Burnside's Bridge because of the notoriety of the coming battle. The bridge was a difficult objective. The road leading to it ran parallel to the creek and was exposed to enemy fire. The bridge was dominated by a 100-foot (30 m) high wooded bluff on the west bank, strewn with boulders from an old quarry, making infantry and sharpshooter fire from good covered positions a dangerous impediment to crossing.

Antietam Creek in this sector was seldom more than 50 feet (15 m) wide, and several stretches were only waist deep and out of Confederate range. Burnside has been widely criticized for ignoring this fact.^[31] However, the commanding terrain across the sometimes shallow creek made crossing the water a comparatively easy part of a difficult problem. Burnside concentrated his plan instead on storming the bridge while simultaneously crossing a ford McClellan's engineers had identified a half mile (1 km) downstream, but when Burnside's men reached it, they found the banks too high to negotiate. While Col. George Crook's Ohio brigade prepared to attack the bridge with the support of Brig. Gen. Samuel Sturgis's division, the rest of the Kanawha Division and Brig. Gen. Isaac Rodman's division struggled through thick brush trying to locate Snavely's Ford, 2 miles (3 km) downstream, intending to flank the Confederates.^[32]