Fagan was soon transferred to the Trans-Mississippi Theater, where he fought at the battles of Cane Hill and Prairie Grove in command of the 1st Arkansas Cavalry Regiment. He was promoted to brigadier-general on September 12, 1862, and assumed command of a brigade composed of the 34th Arkansas, 35th Arkansas, 37th Arkansas, and Hawthorn’s Arkansas infantry regiments. Fagan played a central role in the Battle of Helena, where he and his Arkansas brigade made repeated frontal assaults on United States artillery batteries. During the Little Rock Campaign, Fagan was given temporary command of Price's division.