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Rushden almost took the lead in the first minute when good work by David Bell set up Gary Mulligan, but the striker completely mis-hit his shot.
But they did take the lead after three mintes when fine work by Andy Sambrook caused problems in the Scunthorpe defence - who were sloppy and panicky when trying to clear the ball, and the ball fell for Mulligan to shoot home from 12 yards.
Scunthorpe looked ragged in the opening stages as Rushden played some of their best football of the season - belying their position close to the relegation zone going into the game.
After 23 minutes Scunthorpe should have equalised when Billy Turley punched out to the unmarked Steve Torpey, but the veteran striker shot well wide.
United did get an equaliser eight minutes later when defender Andy Butler powerfully headed home Peter Beagrie's corner.
Rushden almost went aback head in the 44th minute when great work between Bell and Stuart Gray ended with the latter hitting the base of the post and the ball rebounding to safety.
Iron boss Brian Laws made a change at the break, replacing Cliff Byrne - at fault for the opening goal - with the pacier Nathan Stanton.
Two minutes into the second half Scunthorpe went ahead with almost a carbon copy of their first goal, Butler again heading home Beagrie's corner.
After 52 minutes Paul Hayes almost stole in to score a third, but the striker was inches wide.
In the 77th minute the veteran Beagrie produced some clever work on the left, but his pinpoint cross was headed tamely into the hands of Turley.
Seven minutes later former Iron loanee Phil Gulliver almost equalised for Rushden when his shot on the turn went inches wide.
In the second half the Scunthorpe defence looked more in control and Rushden found it hard to create any clear-cut openings.
Scunthorpe put the game beyond doubt in the 89th minute when Torpey hit a stunning shot into the roof of the net from the edge of the penalty box.