Fleetwood dominated the first half and had plenty of chances to have gone in front before they did break the deadlock after 15 minutes. Steve McNulty rose unopposed to meet a Dean Howell free kick and plant a firm header past Exeter goalkeeper Artur Krysiak.
The Grecians equalised in the 24th minute with the goal of the game. Liam Sercombe and Alan Gow combined to tee up Jamie Cureton, who lashed a superb first time shot over the head of Fleetwood goalkeeper Scott Davies and into the far corner.
Fleetwood went back in front four minutes before half-time when City fell asleep at the back and Barry Ferguson picked out fellow midfielder Barry Nicholson with a fine through-ball and he slotted it beyond Krysiak.
John O'Flynn levelled matters from the penalty spot with an emphatic finish before the hour, the spot kick won by Cureton after some foul play from Youl Mawene, but despite dominating the second period Exeter could not find a winner.