Patrick Virgo, Dan Gallimore and Joey Dawson all netted in the victory which puts the side joint top of the league with nine points out of a possible nine, with Lincoln City marginally ahead on goal difference - although the Imps have played five games.
Academy Manager Tony Daws said: "We saw an excellent performance from the boys, particularly in the first-half where we quickly gained the momentum and created a number of goal scoring opportunities which should have put the game beyond our opponents by half-time.
"After going 2-1 up, we dominated the rest of the first-half, creating numerous opportunities. In all honesty, we were disappointed that we didn’t score more goals.
"It was a very good performance and result from our players and although the season is still in its early stages, it puts us in to a very good position in the league."
The young side welcomed back Oliver Lobley and Ben Franklin back into the squad following lengthy injury absences for the duo.
Mansfield were quickest out of the blocks and took an early lead after just two minutes when a throw in on the right side was played short before being returned to the thrower. The cross was cleared by Gallimore but the ball was sent back high into the area with interest with the ball landing on the head of a Stags player before being nodded in from close range.
The home side responded very promptly and levelled the scores just three minutes later. Cameron Wilson sent in a left-sided corner which was headed away at the front post by the Stags before Gallimore headed the ball back into the six-yard box. Ethan Young looked to help the ball on before the ball was allowed to bounce, while Oliver Kemp went for the spectacular overhead kick, but just as he was midair, Virgo nodded the ball into the net.
United would then go ahead for the first time soon after with just 11 minutes on the clock. The home side were awarded a free-kick 30-yards from goal. The wall initially did its job, charging down a low free-kick from Wilson, but the ball spun right to Gallimore who hit his effort low, across goal and into the corner of the net.
From there, it was a dominant first-half performance from the home side, with no fewer than 10 shots heading towards the Mansfield goal, six of which were on target. United were thwarted from adding to their 2-1 scoreline though, and went in at the interval with just a single goal lead.
The Iron's third goal was sublime, with the side turning defence promptly into attack in the 69th minute with Mansfield searching for an equaliser. Wilson intercepted a loose ball and played one pass down the right side of the attacking half. Dawson peeled away from his marker to latch onto the ball before the forward spotted the Stags goalkeeper off his line and took an effort first time from 30 yards, lifting the ball over the shot stopper before seeing the shot nestle in the net making it five goals for the campaign for the 17-year-old.
The Stags narrowed the deficit back to one goal with seven minutes remaining when play came down the right side before a cross was taken down neatly on the right side of the six-yard box before an effort was drilled low and hard across goal.
Despite Mansfield throwing bodies forward in the final minutes of proceedings, Scunthorpe would hold on and remain resoluter to take all three points.
IRON: Balme, Baker, Dawson (Cribb, 79), Gallimore, Kemp, Lewis (Lobley, 54), Moore-Billam (Franklin, 54), Virgo, Wilson, Young, Moore.
IRON UNUSED SUBS: Crosher, Elliott-Bell.
The side are next in action on Tuesday when they travel to face Grimsby Town in the first round of the FA Youth Cup. The match will be played behind-closed-doors at Blundell Park (2.00pm kick-off).