Hooper’s 30th-minute effort – a finish from the egde of the box – proved to be enough for the Iron, who ended a string of six games without success.
The home side did well to overcome the early loss of keeper Joe Murphy, and despite handful of scares were just able to protect their lead.
Coventry should have twice taken the lead inside 10 minutes.
The first chance came when Leon Best found himself one-on-one with Murphy, but he fired straight at the keeper rather than squaring to Clinton Morrison.
Then Best found himself in a similar position and after his first effort was blocked, his second was saved.
And Late on sub Gary Madine twice missed from six yards out as Scunthorpe hung on.