In 1861 Sully was serving on the northern plains against the Northern Cheyenne and Sioux. He commanded troops in the Dakota and Nebraska Territories near Fort Pierre, Fort Kearney, and Fort Ridgely, Minnesota, until the start of the war in the East. He served in the 1862 Peninsula campaign, at Yorktown and at Seven Pines, and during the Seven days, at Malvern Hill. At Antietam, he led his regiment after which he received his rank of brigadier general. As a brigade commander, he served at Fredericksburg and at Chancellorsville. However, his actions at Chancellorsville led to his relocation back to the Northwest.