The Iron had three efforts chalked off for offside but a goal on the hour mark ensured they bounced back from Saturday's 4-0 reverse against Exeter in excellent fashion.
Jeff Hughes had rattled the post for the hosts but chances were few and far between with David Mirfin and Niall Canavan keeping the Fleetwood frontmen quiet.
Scunthorpe broke the deadlock, against the run of play and it was Sam Winnall who notched his fourth of the season. Fleetwood took too long to clear their lines and Winnall's effort cannoned off a red shirt on the way past goalkeeper Scott Davies from 25 yards.
Before that the hosts should have gone ahead, but Sam Slocombe stood tall in the Scunthorpe goal to deny Hughes.
The Iron stopper was having an inspired night, also keeping out Gareth Evans and Antoni Sarcevic before the visitors struck.
From then on Brian Laws' side dug in and defended their lead. Substitute Jamille Matt found the back of the net for Fleetwood but his effort was flagged offside.
Fleetwood threw three strikers into the mix late on but could not break down a resolute defence.
Deon Burton came close to adding a second for the visitors, the substitute sending his shot spinning over the angle having escaped the attentions of Liam Hogan.