Two goals in eight minutes before half-time did the trick for the home side, while Oldham were left cursing their luck after twice getting the ball in the net only to be frustrated by an offside flag.
Scunthorpe opened brightly, attacking the visitors with pace and were finally rewarded in the 26th minute when midfield man Grant McCann rifled home a free-kick from 25 yards.
Oldham were stunned again in the 34th minute when Scunthorpe made it 2-0 after leading marksman Gary Hooper netted his 18th goal of the season by squeezing a close-range shot past goalkeeper Greg Fleming and into the net via the inside of a post.
Oldham thought they were back in the game in the 39th minute when striker Lee Hughes leapt highest in a crowded box to head home a free kick from Danny Whitaker only to be denied by an offside flag.
Scunthorpe started the second half brightly with midfield man Matthew Sparrow going close before the visitors were frustrated again by an offside flag in the 56th minute after winger Chris Taylor had steered the ball from close range.
The Lancashire side were unable to recover as they slumped to a second successive defeat on their travels.
In the closing stages it was Scunthorpe who could have finished more clear-cut winners with both Hooper and substitute Sam Togwell both denied by good saves from goalkeeper Fleming.
It was Scunthorpe's third home win on the trot and lifts them to within one point of second place in the table behind runaway leaders Leicester.