Harris Flanagin was born in Roadstown, New Jersey. Flanagin was educated in Quaker schools in New Jersey. At age 18 he became a professor of mathematics. Flanagin moved west and opened his own private school in Paoli, Illinois. He studied law and was admitted to the Illinois bar in 1837.
Flanagin moved to Arkansas and entered politics. He served in the Arkansas House of Representatives from 1842 to 1844.
During the American Civil War he served in the Confederate States Army as a Captain and rose to the rank of Colonel before the conflict was over. He served with the 1st Arkansas Infantry Regiment.
In 1862 Flanagin was elected Governor of Arkansas and was recalled from active duty to take office. His administration dealt primarily with war related measures and maintaining order and continuing government while undergoing an invasion. His administration was faced with shortages of critical items, rising prices, care of fallen soldier's families, and related problems. During the war the government was forced to suspend the collection of taxes and financed the war with paper "war bonds".
The capitol at Little Rock, Arkansas fell to Union troops on 10 September 1863. Flanagin seized as many government documents as he could and fled to Washington, Arkansas where he set up a temporary capitol.
Flanagin left office on 18 April 1864 and returned to his law practice in Arkadelphia, Arkansas. Flanagin is buried at Rose Hill Cemetery in Arkadelphia.