A disappointing crowd of 4,616, the lowest of the season, saw a dogged encounter between the two relegation candidates.
Scunthorpe striker Martin Paterson had an early shot saved and Preston keeper Andy Lonergan kept another shot out with his legs.
After 20 minutes Simon Whaley fired over a right-wing cross to Neil Mellor who mis-kicked when it was seemed easier to score.
Matthew Sparrow had a close-range shot saved and when the rebound fell to Ian Morris he fired wide of the keeper's left-hand post.
Kevan Hurst then saw his 20-yard shot saved by Preston keeper Lonergan who dived low to his left to keep it out.
Seven minutes before the interval Jack Cork had a weak shot easily saved by the Preston keeper before North End's Darren Carter was denied by Scunthorpe keeper Joe Murphy.
Preston capital Paul McKenna started the second half with a throughball to Whaley who was on the right-hand side of the penalty area.
He hit a right-foot shot from five yards out beneath the keeper and into the back of the net to make it 1-0 to Preston after just two minutes of the second half.
Paul Hayes had a 20-yard shot saved by the Preston keeper and ex-Liverpool striker Mellor also went close to doubling the home side's lead.
Scunthorpe had to substitute the injured Marcus Williams after 66 minutes and he limped off to be replaced by Jonathan Forte.
Whaley had another shot saved before Scunthorpe keeper Murphy had to go off with a suspected dislocated finger and was replaced by Josh Lillis.
Scunthorpe captain Andy Crosby had a 12-header saved and Lonergan also denied Hayes an equaliser.
In the closing stages the Iron's Ian Morris had a 25-yard right-foot shot which flew narrowly wide of the keeper's left-hand post as Preston hung on.