Flynn, 28, who fell out of favour at Huddersfield after just one season, had his contract at the Galpharm Stadium terminated by mutual consent on Tuesday. He is likely to start alongside Lee Bullock in central midfield when City take on Sven-Goran Eriksson's Notts County this weekend.
And the former Gillingham midfielder admits the lure of working under McCall was a big factor in his decision to drop into League Two.
Flynn told the club's official website: "He's a passionate man who had a great career and it's always flattering when someone like Stuart McCall wants to sign you.
"When he first came in for me a couple of years ago I also got an offer from Blackpool who were in the Championship which was something I couldn't turn down. But he's an ambitious manager and I feel that Bradford are a very good club for this league.
"I didn't know the significance of the number four shirt here but it was good for me when I wore it for Gillingham and scored double figures in League One, so hopefully I can get more than 10 this season."