United fell behind after two minutes, as a ball was played down the left side of the defence and Ethan Young came across and upended a home striker, getting booked for it. They took a free-kick just to the right of the centre of the goal, and bent the ball around the wall. Jake Balme made a save but couldn't hold onto it and a Burton player latched on to the loose ball and tapped home.
Scunthorpe had a chance in the 19th minute as Harry Lewis did well, putting a cross in from the left that Jack Moore-Billam connected to, having a good shot which the goalkeeper saved.
After 22 minutes, the Iron equalised as they pressed high up the pitch, winning the ball back. Tyrell Sellars-Fleming did well to put a good cross in from the left hand side to the far post, and Nat Wallace came in from the right wing to finish off.
In the 29th minute, United nearly went in front as Sellars-Fleming turned on the edge of the box and shot just over the crossbar.
Then, two minutes later, Scunthorpe were on top and went 2-1 up as a fantastic passing move down the left-hand side ended with Sellars-Fleming sidefooting home at the far post.
On 34 minutes, Burton won a corner and put it into the box. Josh Robertson came and attacked the first ball, putting a good header on it, and Moore-Billam helped to clear it before one of their players latched onto the loose ball and capitalised on United being slow to come out and block the shot, with the ball flying into the net for the equaliser.
With 57 minutes gone, the Iron went in front when Lewis got free down the left and put a deep cross into the far post, which Wallace met coming in from the right wing, sidefoot volleying into the net for his second goal of the afternoon.
Five minutes later, Scunthorpe could have put the game to bed when Moore-Billam sent a corner in and Robertson got up just outside the six yard box, making good contact but placing his header just past the post.
Soon after, Lewis then cut in from the left on the edge of the box and fired an effort just wide.
Straight after those missed opportunities, the hosts attacked through the middle and a shot from the edge of the box snuck in to make it 3-3.
Then, soon after, Scunthorpe went 4-3 down as Burton broke down the left and put a cross into the far post which was cleared to the edge of the box, but United were too slow to come out and block the shot, which was converted home.
The Iron piled forward to try and get an equaliser and left themselves a little bit open at the back, as Burton played a long ball forward which one of their strikers managed to run onto and score the decisive goal.
Academy manager Tony Daws said: "The lads were absolutely gutted at the end but it's a great learning curve because even if you've lost at youth level, you can learn a lot from losing.
"They were still pushing at the end to try and level in what was a great game of football, but you don't always get what you deserve.
"There were lots of positives to take from the performance and we all felt we deserved to win, but it's important they learn from this game for future."
The Under-18s return to action with a home match against Harrogate Town next Saturday.
IRON: Balme, Wallace (Elliott-Bell, 75), Lewis, Young, Moore, Lobley, Moore-Billam, Cribb, Sellars-Fleming, Poulter, Robertson.
IRON SUBS NOT USED: Pike, Foster, Strouther, Burden.