Paddy Madden thought that he had given the hosts the lead inside the opening quarter of an hour when he fired the ball into the back of the net, but his effort was ruled out for offside.
A dominant spell from Fleetwood gave the visitors a corner, but David Ball missed a free header from close range.
Conor McLaughlin tried a long-range effort for Fleetwood on the half-hour mark, but Bobby Olejnik, who joined the side on loan from Peterborough United earlier today, watched it all the way for a comfortable save.
Ball and Steve Schumacher also had chances before the break, but Scunthorpe did enough to keep the scores level at half time.
Fleetwood continued to look the more likely to score in the second half, and finally broke the deadlock in the 70th minute when the ball fell to Jamie Proctor at the back post for a simple tap-in.
The visitors doubled their advantage 10 minutes later when Schumacher picked out Gareth Evans for a header from close range in the final 10 minutes.
Niall Canavan almost pulled one back in stoppage time for the hosts, but his header bounced back off the post to ensure that Fleetwood secured the win.
The result leaves Fleetwood top of the table with a 100% record, while Scunthorpe are bottom.