Graham Alexander’s men twice let the lead slip as they were held at home by the Iron.
Fleetwood were quick to put Saturday’s disappointment behind them, grabbing an early lead when Jamie Proctor rose to nod home Nick Haughton’s free kick in the third minute.
Town could easily have had a second moments later, Proctor selfess on the edge of the box, picking out the run of Gareth Evans whose low drive was scooped up by Iron keeper Luke Daniels.
Gary McSheffrey created a brief moment of panic in Town’s otherwise cool and collected back line when he stormed through on the end of a quick break - Chris Maxwell to the rescue with a diving save, diverting the shot with his feet.
Fleetwood had half chances to add to their tally but will wish they’d done more, Scunthorpe levelling right on half time.
An over-run pass handed the Iron the initiative, the visitors breaking in numbers, led by former Seasider Isaiah Osborne, McSheffrey with time to place a shot into the corner from 18 yards.
Fleetwood’s spirit wasn’t broken by the late blow and a mistake by Osborne almost gifted them a second.
His sloppy clearance fell at the feet of Proctor, Evans slipped in at the back post, his blast goal-bound but somehow blocked inside the six yard box.
The home side did regain their advantage when Josh Morris curled the ball home from 18 yards after a knockdown from sub Liam McAlinden.
But the lead lasted little more than a minute, Scunthorpe’s George Evans not closed down and sending a low deflected drive into the Fleetwood net.
Maxwell almost landed himself in trouble, caught in possession after misjudging a backpass as the two sides traded blows, both sensing late drama under the Highbury lights.
With time running out Town nearly grabbed a third, Conor McLaughlin losing his feet but keeping the ball, hooking a pass to Liam McAlinden who got tangled two yards out, somehow unable to bundle a shot past Daniels.
The game ended in controversy, referee Nigel Miller calling time with Fleetwood inside the Scunthorpe box, denying any chance of a last ditch winner.