Andy Morrell put Wrexham ahead from the penalty spot just before half time after Cliff Byrne had tripped Darren Ferguson on the left edge of the area.
Morrell stepped up confidently to send keeper Tom Evans the wrong way and claim his 19th league goal of the season.
Scunthorpe had lots of possession but Wrexham had the chances and sharp shooter Lee Trundle might have done better with an early shot that flew over the bar.
He set up Morrell for another shot that was deflected for a corner and when winger Paul Edwards had a chance he headed over the top.
Evans made a good save to deny Morrell a second goal and then dived to clutch a close-range shot from Trundle.
Again the Scunthorpe defence was in trouble when Trundle powered in for a shot which the keeper turned for another corner.
United's task was made more difficult when Andy Dawson was shown a second yellow card for fouling his tormentor Carlos Edwards and was sent off.
Two minutes later Trundle confirmed Wrexham's dominance, finishing off a good move started by Ferguson, rounding the keeper and tapping in from close range.
When Matt Sparrow finally found the net for Scunthorpe with a shot that flew in off the post, it was too late to save the game.
Wrexham manager Denis Smith said: "It was a good result and until we went 2-0 up we gave a good performance.
"We didn't give them any chances until the last few minutes when we eased off and had defensive problems. "A disappointed Brian Laws said: "We are a lot better side than we showed today. We had two players suspended and our target man Steve Torpey was out injured."He said he had no complaints about the red card, but about the penalty he said: "I think the referee was conned."