Flynn previously played in Major League Baseball (MLB) for the Miami Marlins and Kansas City Royals.

[6] On July 23, 2012, Flynn was traded to the Miami Marlins with Jacob Turner and Rob Brantly in exchange for Omar Infante and Aníbal Sánchez.

On November 28, 2014, the Marlins traded Flynn and Reid Redman to the Kansas City Royals in exchange for Aaron Crow.

Flynn was assigned to the Omaha Storm Chasers of the PCL and on April 9 suffered a torn lat muscle in his first and only 2015 appearance.

Flynn surrendered two runs on three hits, struck out two and walked two over 4.0 innings in a relief appearance against the Cleveland Indians.

[15] In 2017, Prior to the start of spring training, Flynn suffered a broken rib and three fractured vertebrae when he fell through the roof of his barn, and was ruled out for at least eight weeks.