In 1957, Flournoy took a faculty position in the Pomona College Department of Political Science, where he quickly won tenure and remained a full time professor until 1960 and a part time faculty member until 1966, when he ran for California State Controller.

In 1960, he successfully ran for California State Assembly as a Republican Party candidate, and served from 1961 to 1967.

Flournoy blamed his loss on President Gerald Ford's pardon of Richard Nixon in September, 1974.

After retirement he resided in Ponte Vedra Beach, Florida, and Bodega Bay, California.

Flournoy died of congestive heart failure on January 7, 2008, on a flight from San Diego to Santa Rosa, California.