The 30-year-old was forced off during Saturday's 2-1 home win over Aldershot due to a hamstring injury.
The full extent of the damage is not yet known, but with only 12 days of the season left Flynn has played his last game.
The Welshman has endured a disappointing campaign, missing the first two months after undergoing surgery last summer to resolve a hernia problem, while the Bantams only ended their relegation fears with victory on Saturday.
Source: PA
Source: PA