Fowle was opposed to secession, but he still volunteered as a
private in the North Carolina
Militia. He was soon appointed
major in the commissary branch. He resigned that post and helped to raise the 31st North Carolina Infantry regiment. On September 9, 1861, Fowle was appointed
lieutenant colonel of the regiment. In February 1862, Fowle and the 31st NC were captured on Roanoke Island. He was paroled two weeks later. In September 1862, he was defeated in the election for
colonel of the regiment and left the
Confederate States Army. In October, he was elected to the state legislature representing
Wake County, North Carolina. In March 1863, Governor
Zebulon B. Vance appointed Fowle
adjutant general of North Carolina with the rank of
major general. Fowle resigned the post in the fall of 1863 after a disagreement with Vance. Fowle was reelected to the legislature in 1864. ==Post-War==