The Iron Under-18s were beaten 2-0 at Huddersfield Town on Saturday morning.
United conceded after six minutes as a cross came in from the left and was tapped in at the far post.
Tyrell Sellars-Fleming had a one-versus-one in the 19th minute, but forced a really good save from the Terriers goalkeeper.
In the 28th minute, Scunthorpe hit the post as the ball was transferred from the left side to the right, with Harvey Cribb coming in and striking the ball well. It went past the goalkeeper but hit the post and came back into his hands.
For the majority of the second half, the Iron played well and were in possession and dictating the game, hitting the post again through Ben Franklin.
Huddersfield scored very late on to make it 2-0 with a sucker-punch goal.
Academy manager Tony Daws said: "Prior to then we had several very good chances, playing with a good tempo. It was just the final cross or pass not quite being good enough that meant we didn't take full advantage on the day."
IRON: Foster, Wallace (Abraham, 53), Lobley (Strouther, 66), Moore, Pike, Young, Cribb, Robertson, Sellars-Fleming (Burden, 73), Poulter, Franklin.
IRON SUBS: Balme.