The first concert is taking place at 8 p.m. Thursday at Fox Theatre in Redwood City, with tickets starting at $50.
Flannery and his band the Lunatic Fringe will also play three more shows, on Friday at the Sweetwater Music Hall in Mill Valley; on Saturday at Napa's Uptown Theatre; and on Sunday at Kuumbwa Jazz in Santa Cruz, Stow's hometown.
Stow, a paramedic and father of two, suffered a serious head injury in the March 31, 2011, attack outside Dodger Stadium. Two men, Louie Sanchez and Marvin Norwood, were arrested months later and are awaiting trial.
Flannery, who has been a coach during both of the Giants' recent World Series wins in 2010 and 2012, has raised about $70,000 to help with Stow's medical bills and held a large benefit concert last year in Napa with Bob Weir from the Grateful Dead, according to team officials.
Stow's family, who has posted regular updates on his progress on the website www.support4bryanstow.com, wrote a post earlier this month mentioning Flannery's efforts and others who have helped to raise money for Stow.
"We are still so humbled by the fact that, even though it's almost been two years, people have not forgotten and still want to support Bryan and his family," the post read.
More information about Flannery's shows and how to purchase tickets available on his website at www.timflannery.com.