Notable for heading the Council for Secular Humanism and for editing the organization's Free Inquiry publication, Flynn is also known for his contributions to the Free Thinking blog and to The New Encyclopedia of Unbelief. His full-length works include The Trouble with Christmas and the satirical science fiction novel Galactic Rapture.
After graduating from Xavier University in Ohio, he began to doubt his long-held Roman Catholic beliefs and to forge a life and career in accordance with his new atheistic stance.
He produced a television documentary series titled American Freethought.
Born and raised in Erie, Pennsylvania, he later settled in Buffalo, New York.
His passion for activism on behalf of atheism, secular humanity, and free thought developed from his early reading of Robert Ingersoll's work. Later in his life, Flynn managed the Robert Green Ingersoll museum.