John Flannagan, Jr. was was born on February 20, 1885 near Trevilians in Louise County. He attended public schools and graduated from the Law Department of Washington and Lee University in 1907. He was admitted to the bar that same year and began his law practice in Appalachia.

He served as Buchanan County's Commonwealth Attorney in 1916 and 1917. He moved to Clintwood in 1917 where he practiced law until 1925. He then moved his law practive to Bristol. Flannagan was elected as a Democrat to the 72nd Congress and to the eight succeeding Congresses, serving from 1931-1949. During the 72nd and 79th Congresses, he was chairman of the Committee on Agriculture. He was a congressional advisor to the first session of the Food and Agriculture Organization of the United Nations (UN) in 1945.