Jack Sowerby gave the hosts a 21st-minute lead but goals from Alex Gilliead and Shay McCartan in the space of seven second-half minutes earned the fifth-placed Bantams victory.
Fleetwood started well, with Ashley Hunter, Sowerby and Jordy Hiwula all creating chances in the opening six minutes.
And Town went ahead when ex-Bradford man Hiwula teed-up Sowerby to coolly slot home.
Fleetwood should have been further ahead after dominating the first half and were punished after the break.
Uwe Rosler’s men lost the ball after playing a short corner and a Bradford break was finished off by on-loan Newcastle midfielder Gilliead in the 56th minute.
And seven minutes later the visitors led. Tony McMahon’s corner found Charlie Wyke at the back post and the striker nodded the ball into the path of McCartan who curled in.
Conor McAleny wasted a golden opportunity to level eight minutes from time as fellow substitute Wes Burns’ deflected shot fell to him at the back post but he cannoned the ball wide as Fleetwood slipped to a third successive home league defeat.
Colchester will hand late fitness tests to Ryan Jackson and Brandon Comley prior to their clash with Yeovil.
Arsenal secured their place in the quarter-finals of the Europa League following their 3-1 defeat of AC Milan at the Emirates Stadium on Thursday.
Danny Welbeck scored twice against AC Milan to toast his England recall by sending Arsenal into the last eight of the Europa League.