The Iron's youth team were beaten 3-2 by their Doncaster Rovers counterparts at Cantley Park on Saturday morning.
The juniors went a goal down on five minutes when the hosts scored with a free-kick from the edge of the 18-yard box.It was then 2-0 in the 33rd minute when United conceded from a short corner.
Scunthorpe pulled one back in the 44th minute when Jamie Wootton got on to a throughball from Lewis Akeister.
However, Doncaster's two goal advantage was soon reapplied on 52 minutes when the Iron were caught out by a long ball and Rovers went on to score from it.
Zac Cowling pulled another back in the 72nd minute after a good cross from Hakeem Adelakun found him.
The away team had a couple of late chances but couldn't find the equaliser.
"We perhaps should have done better with those opportunities," said youth development officer Tony Daws.
"We are disappointed to concede from two set-plays which cost us the game.
"The lads haven't realised how important it is to be responsible and do their jobs and defend set plays better.
"However, in the second half we played well."