Billy was born in Green Bay, Wisconsin. In 1970, a local blues club opened and Flynn was inspired by the music provided there by Luther Allison, Johnny Littlejohn and Mighty Joe Young. Flynn was fortunate to be spotted playing outside the venue by Jimmy Dawkins, who arranged for Flynn to play with him on stage. Flynn joined Dawkins's backing band in 1975, and he played and toured with them until the end of the decade.
Flynn also worked locally during this period and played alongside Sunnyland Slim. In the early part of the 1980s, Flynn was a member of the touring ensemble, Jim Liban and the Futuramics. In the late 1980s, he joined the Legendary Blues Band. He also played with Mississippi Heat.
In addition to his own work, he has worked and recorded with Bryan Lee, Little Smokey Smothers, Mark Hummel, Willie Kent, Snooky Pryor, Big Bill Morganfield, John Brim, Jody Williams, Little Arthur Duncan, Deitra Farr, Willie “Big Eyes” Smith, Kenny “Beedy Eyes” Smith and Billy Boy Arnold.