Flynn graduated from St. Xavier College in 1893 where he played college baseball.
Flynn made his National League debut with the Cincinnati Reds on July 17, 1894 in relief of Lem Cross in a game against the Cleveland Spiders. Flynn, who told friends before the game that he was not feeling well, allowed seven runs during the eighth inning. He started his next outing on July 29 and, according to The Cincinnati Enquirer, was "was too badly shaken up with stage fright to do himself justice." He pitched poorly in a short outing before being relieved by Tom Parrott. He would not appear in a game for the Reds again.
Flynn spent 1895 pitching in Richmond, Virginia in the Virginia State League and won twenty-five games. He was picked up by the New York Giants at the end of the season.

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