His father died during his youth and his mother, Catherine A. Fagan, in 1842 married Samuel Adams, who became acting governor of Arkansas two years later.

Fagan served in the United States Volunteers during the Mexican–American War with Company C, Arkansas Mounted Infantry Regiment, under Colonel Archibald Yell and was promoted to the rank of second lieutenant.

[citation needed] 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.

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.

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.

[citation needed] He was appointed United States Marshal by President Ulysses S. Grant in 1875, working for "Hanging Judge" Parker.

In this capacity, Fagan recruited Bass Reeves as the first black deputy marshal to work west of the Mississippi River.