Early goals Jack Dyche and Billy Kee set the visitors on their way, before trialist Piteu Crouz scored from the spot to add gloss to the scoreline.
The Millers did create a number of good chances coming close through Kuda Muskwe and Darnelle Bailey-King, but were powerless to resist as the visitors prevailed 3-0 winners.
Piteu Crouz got the first sight of goal after some clever footwork on the right flank saw him come inside and flash an effort inches wide of Scott Loach's far post.
The visitors took the early incentive with Crouz the architect again as his low effort could only be parried by Loach into the path of Dyche who made no mistake from close range to put the Iron ahead.
The Millers had to wait until the 20 minute mark for their first sight of goal which came when Jerry Yates saw Sam Slocombe off his line before attempting a lob from 30 yards that went just wide of the target.
The Iron threatened again when Dyche took aim from goal from 20 yards before a neat passage of play saw Kieran Bywater denied by a good block.
Their persistence finally paid off when a cross from the left was stabbed goalwards by Dyche before Kee made the vital contact from point blank range to turn the ball home and double Scunthorpe's advantage.
The hosts had a superb chance just before the interval when Darnelle Bailey-King was released down the right flank before he clipped a ball over the onrushing Slocombe that went agonisingly wide of the near post.
Half-time: Rotherham 0 v 2 Scunthorpe
It was the hosts who took the initiative after the break as an early corner provided two big chances for the young Millers side.
Danny Rowe went close with a volley before Dan Smalley produced a cross which was inches too high for Kuda Muskwe who had the goal at his mercy.
Moments later Muskwe found a way through the Iron defence with a clever run that saw him beat two visiting defenders before skewing a left footed effort on the edge of the area.
Yates was then presented with the opportunity to set his sights on Slocombe's goal with a free kick 20 yards out following a fould on Rose, but the Millers forward curled his effort high over the wall and over the crossbar.
Scunthorpe created their best chance of the half when Charlie Cleminshaw met a cross from the left flank and headed at goal only to be denied by a super save from Loach.
The Iron added a third against the run of play after Crouz was hacked down in the penalty area.
The Leeds United trialist picked himelf and dusted himself down before keeping his cool to slot beyond Loach from the spot.
Bailey-King then made inroads down the right hand side before lofting the ball over Slocombe who had come out to close him down. However, he couldn't convert the chance from a tight angle, firing a volley just wide of the near post.
The Millers had another big chance to pull one back when a cut back from the byline allowed Muskwe an effort on goal but he was denied by Slocombe from 15 yards.
Muskwe continued to prove a thorn in the Iron's side and almost got rewarded for his industry when a ball over the top allowed him a strike on goal which fizzed over the crossbar.
Full-time: Rotherham 0 v 3 Scunthorpe
Millers: Loach, Bailey, Smalley, Dickinson (Shelley 75), Rowe, Peace-McDonald, Bailey-King, Warren (Fenton 30), Muskwe, Yates, Johnson (Rose 12).
Unused: Bilboe, Norfolk, Lucas.