Preston received a welcome break from the Championship as Simon Whaley's solitary strike ensured they progressed to the FA Cup fourth round.
Simon Whaley scored his fourth goal in eight games for Preston
The Lilywhites are bottom of the Championship table but Whaley's second-half goal lifted the gloom.
Scunthorpe had the better of the first half with Martin Paterson, Matt Sparrow and Ian Morris close to scoring.
But Whaley sealed victory when he guided a right-foot finish into the bottom corner from close range.
Preston had lost three consecutive games ahead of the visit of Scunthorpe and had suffered defeat at home in the league to the visitors on Boxing Day.
Scunthorpe were the more threatening and midway through the first half goalkeeper Andy Lonergan had to be alert to stave off Sparrow's close-range effort.
Less than a minute later, Morris forced Lonergan into a fine reflex save with a menacing right-footed strike.
Preston finally managed to create a chance of their own but Whaley was unable to keep Lewis Neal's cross on target.
Paul Hayes's shot whistled past the post just after half-time, but it was the home side who took the lead in the 47th minute.
Midfielder Paul McKenna neatly found Whaley, who scored for his fourth goal in eight matches.
Neil Mellor could have doubled Preston's lead but the former Liverpool striker was unable to do justice to Youl Mawene's fine cross.
Scunthorpe had a chance to earn a replay but Morris's long-range effort in the final minute of normal time was wide of the target.
Preston: Lonergan, Davidson, Mawene, Chilvers, Hill, Whaley, Carter, McKenna, Lewis Neal, Mellor (Ormerod 87), Hawley.
Subs Not Used: Chris Neal, Nicholls, Anyinsah, Sedgwick.
Goals: Whaley 47.
Scunthorpe: Murphy (Lillis 72), Byrne, Crosby, Martis, Williams (Forte 66), Sparrow, Cork, Morris, Hurst, Hayes (Ameobi 86), Paterson.
Subs Not Used: Seck, Taylor.
Ref: Colin Webster (Tyne & Wear).
BBC Sport Player Rater man of the match: Preston's Whaley and McKenna 9.00 (on 90 minutes).
Please note that you can still give the players marks out of 10 on BBC Sport's Player Rater after the match has finished.