The hosts replied with Anthony Pilkington seeing a free-kick well gathered by Joe Murphy and then, on 20 minutes, Pilkington was involved again as he headed over at the far post from Jim NcNulty's out-swinging cross.
The Iron fluffed a great opportunity to score on 23 minutes. Cliff Byrne lifted the ball into centre-half David Mirfin who was in acres of space in the Stockport box. However, he dithered before shooting and allowed Fon Williams to make the save.
The visitors broke the deadlock after half-an-hour. McCann played a neat ball to Hooper, and he held off the attentions of Stockport skipper Gareth Owen before firing home low across the body of Fon Williams and into the corner of the net.
Stockport's best chance to equalise before the interval came from Gary Dicker when he side-footed over from the edge of the box.
It took Scunthorpe less than a minute after the restart to double their lead. Paul Hayes miscued his shot from 12 yards, but Hooper was there to mop up the loose ball at the far post for his second goal of the game.
The visitors then made it three on 58 minutes. Thompson was fouled on the edge of the Stockport box, and up stepped McCann to curl the free-kick into the top corner.