Lee Martin fired the visitors ahead in the opening half, but Josh Morris scored an equaliser soon into the second period.
However, Josh Parker and Tom Eaves both netted to seal victory for Steve Lovell’s side.
United manager Graham Alexander opted to name an unchanged XI from the team that secured a 1-1 draw at Portsmouth last weekend.
The away side started brightly, and fashioned a few dangerous crosses, but the Iron defended well to see away the danger.
The first major opportunity fell for Eaves after 12 minutes, but he could only head wide from a dinked Bradley Garmston cross on Gillingham’s left wing.
The Iron should have been one ahead after Morris crossed dangerously, but an unmarked Neal Bishop could only head over.
United continued their dominance, firstly when Cameron Burgess had a header cleared off the line – before the resultant corner saw a scramble, ending in a superb block from the Gills defence to keep the score level.
The visitors went ahead after they dispossessed the Iron and played into Parker, before Martin was set up to hammer it into the top corner.
The home side were afforded a half chance five minutes before the break after Kevin van Veen’s ball made it all the way to the back post, but Burgess could only prod wide.
The scores should have been level a few minutes later, but somehow a Gills defender got his body in the way of Charlie Goode’s thunderous strike.
The Iron could have had a penalty as half-time approached, but referee Carl Boyeson deemed Parker’s trip on Duane Holmes to be narrowly outside the box. Morris’ resulting free kick was dealt with confidently by the visiting defence.
Morris almost found an early second-half leveller from a free-kick not far from the edge of the visitors’ box, but the ball didn’t dip enough to hit the target. A great effort nonetheless.
It only took Morris an extra minute to hit the target this time. After he picked up a pass from Tom Hopper, he hit it from the edge of the box past Tomas Holy to make it 1-1.
The Gills could have been ahead again soon after the equaliser, but Rory Watson was the hero as he made himself big to put Eaves off when he had a clear sight of goal.
United broke a minute later, and it was Morris again who was teed up – this time by Holmes – but his curled effort was deflected onto the post.
Gillingham were back ahead after a cross from the right was headed home by Parker, leaving Watson with no chance.
Eaves put the visitors 3-1 ahead after being played through on goal, sliding the ball under Watson.
Ivan Toney had his first effort after coming off the bench when Bishop crossed, but his header was held easily by Holy.
Toney wasn’t too far away again with eight minutes left to play, but his header went narrowly wide this time.
There were five additional minutes added on, as United looked to find a way back into the game. It wasn’t to be though, and the game ended at 3-1 to the visitors.
TEAM LINE-UPS
Scunthorpe United: Watson, Wallace (C), Ojo, van Veen, Morris, Bishop (McGeehan, 78), Hopper (Toney, 62), Adelakun (Novak, 78), Holmes, Goode, Burgess.
Substitutes not used: Kelsey, Townsend, Lewis, McArdle.
Gillingham: Holy, O’Neill, Garmston (Ogilvie, 87), Ehmer, Zakuani, Hessenthaler, Eaves (Wilkinson, 78), Martin (C), Parker, Reilly, Byrne.
Substitutes not used: Nelson, Lacey, Nugent, Oldaker, List.
Attendance: 4,905.
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