At the start of the American Civil War, Fagan raised a company for the
Confederate States Army and became its
captain. When his unit was folded in with the
1st Arkansas Infantry Regiment on May 6, 1861, the very day that
Arkansas seceded from the
Union, he was elected as
colonel of the combined 900-man regiment. They were formally mustered into service in
Lynchburg, Virginia in May 1861. His regiment was a part of the first wave of Confederate attacks under General
Albert Sidney Johnston at the
Battle of Shiloh. He also participated in the
Siege of Corinth, but fell into disfavor with his superior officer, General
Braxton Bragg. 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
Sterling Price's
division. Fagan fought in the
Camden Expedition, including the successful destruction of a Federal supply train at the
Battle of Marks' Mills, which led to the Federal retreat from southern Arkansas. In recognition for his service in the Camden Expedition, he was promoted to
major-general on April 24, 1864, and commanded the Arkansas division of Confederate
cavalry during
Price's Missouri Expedition. His division broke in a "disgraceful manner" during the failed assault on
Fort Davidson at Pilot Knob, Missouri. During Price's withdrawal from Missouri and Kansas, Fagan and
John S. Marmaduke's divisions were overwhelmed at the
Battle of Mine Creek. The end of the war found Fagan in command of the District of Arkansas of the
Trans-Mississippi Department, which was active militarily until late April 1865. == Later life ==