Midfielders Flynn and Mitchell have agreed to cancel their contracts and forward Fagan is in the process of doing so at Valley Parade.
Flynn, 31, joined the Bantams in August 2009 after leaving Huddersfield and played 104 games, scoring 14 goals.
Fagan, 29, netted eight times in 35 games after joining in September - the third time he had teamed up with Parkinson.
Mitchell, 23, signed last summer from Falkirk, scored once in 16 appearances and has not played since the JPT defeat at Oldham in December.
