Goals from Murray Wallace and Hakeeb Adelakun, either side of a Callum Cooke strike secured the points for the hosts, who bounced back from the weekend loss at Port Vale.
The Iron went into the game making six changes from the side that lost at Port Vale, as Joe Anyon, Charlie Goode, second year youth trainee Lewis Butroid, Adelakun, Sam Mantom and Paddy Madden came in for Luke Daniels, David Mirfin, Conor Townsend, Neal Bishop, Stephen Dawson and Kevin van Veen.
Duane Holmes almost got the hosts off to a flying start when he burst through on three minutes. The American was played through nicely by Tom Hopper, but he couldn’t finish - firing wide from the left corner of the box.
United were by far the dominant side in the opening stages of the match, and created another opportunity shortly after, when the returning Madden was teed up on the edge of the penalty area via a sliced clearance. The Irishman got his effort on target, however it was well held by Boro stopper Joe Fryer.
Holmes was then involved again, just after the mid-way point. The midfielder seized on a lapse in concentration in the visitors’ defence, going for goal moments later. He failed to hit the target though, as he dragged his shot fractionally wide of the goal.
Five minutes before the break, the diminutive No 19 went for goal once more. Following a burst down the right from Jordan Clarke, the ball reached Holmes, who could only manage to poke his attempt wide, from the middle of the penalty area.
Boro held out though, and prevented the Iron from scoring ahead of the interval - as both sides went in level.
Graham Alexander’s side quickly restored their dominance after the restart, with Josh Morris setting his sights from distance. The winger aimed for the top corner, and looked to have the beating of Fryer in the Boro goal, but he got a little too much height on his effort.
Scunthorpe ‘keeper Anyon, who’d been a mere spectator for the majority of the game up until that point, was soon called into action. He had to make a fine save too, tipping a Joao Morelli shot round the post for a corner.
A brilliant bit of play from defender Goode then nearly unlocked the Middlesbrough backline. His superb cross-field ball found Madden, who made a driving run for the penalty area, only to be foiled by some good goalkeeping from Fryer.
Just after the hour mark though, the Iron found a breakthrough. Wallace was the man who got it, towering above everyone to plant his header into the bottom corner of the goal.
The away side went in search of an equaliser, and they went close when Cooke took aim, and drew a smart save out of Anyon, with the United man getting down well to beat the ball away.
Cooke wouldn’t be denied for too much longer however, as on 72 minutes the Boro midfielder found the back of the net with a sweetly struck shot from long range, after the ball had fell to him on the half volley.
As soon as the visitors had finished celebrating though, they found themselves behind once more. Adelakun restored the Iron’s lead, beating Fryer with a strike from 25 yards out.
Goode could have sealed the points in the minutes after Adelakun’s finish, but he could only manage to glance his header wide from a brilliantly delivered corner from the right.
The defender’s miss nearly went on to be punished, by Boro’s goalscorer Cooke, who fired wide from almost exactly the same spot in which he tied the game up.
Cooke’s effort would prove to be Boro’s last attempt on goal, with Alexander’s men holding out for a well deserved victory.
Scunthorpe United: Anyon, Wallace, Madden (Wootton 77), Morris, Hopper, Adelakun, Mantom (van Veen 82), Holmes (Sutton 49), Goode, Clarke, Butroid.
Substitutes not used: Daniels, Mirfin, Dawson, Bishop.
Middlesbrough: Fryer, Espinosa, Cooke, Elsdon, Johnson, Kitching, Morelli (McAloon 84), Morris, Pattison, Tavernier (Mondal 64), Tinkler.
Substitutes not used: Hemmings, McGoldrick, Maloney, Wheatley.