In the spring of 1862, Sullivan commanded a brigade of infantry during the Valley Campaign and led it into action at the First Battle of Kernstown. He was commissioned as brigadier general to date from April 28, 1862. Later in the spring, he was transferred to the Western Theater and assigned command of a brigade in the Army of the Mississippi, serving under William S. Rosecrans. Sullivan again saw combat in the battles of Iuka and Corinth in Mississippi. In the autumn of that same year, Sullivan was given command of the District of Jackson, Tennessee, and its widely scattered garrisons of Union troops. There, his men were often pitted against the raiders of Confederate general Nathan B. Forrest, including the Battle of Parker's Crossroads, December 31, 1862..