Goalkeeper Josh Murtagh had to be alert after just two minutes, as the Lincoln number nine found space in the area before the 16-year-old saved well to his left.
With twenty minutes gone, the Imps came forward again looking for an opener, with the ball falling kindly to the number seven on the right. Murtagh was once more called into action, as he did just enough to prevent the opening goal.
Charley Strouther blazed a free-kick over shortly after, as the Iron looked to create their first real opening in the game.
The visitors then took the lead ten minutes before the interval, as City’s number ten found space to slot the ball home after some tidy build-up play.
As the second half began, Lincoln found their second goal as the troublesome number nine had time for two attempts at goal, before rolling the ball into the next to double his sides lead.
Grayson Giles was presented with a great chance to quickly respond as a misplaced goal kick fell directly to the Iron forward. His effort was well saved however, as the academy outfit looked to get a foothold back into the game.
Strouther did superbly once more on the hour mark, charging forward down the left flank before getting to the byline and cutting the ball back. His pass found Harvey Cribb, whose deflected strike was gathered by the Lincoln ‘keeper however.
Finn Abraham was on hand to prevent what looked to be a certain third goal with less than 20 minutes remaining. The teenager cleared a City effort off the line emphatically to keep the score at 2-0.
But just ten minutes later it was to be three, as the visitors number 11 found space on the edge of the area to fire home via a deflection that had come back off the post.
Giles was again set free in the final ten minutes, twisting and turning after some good work in the build-up from Lucas Dickinson. The striker pulled the ball back onto his left foot before his effort was saved once more.
As the full-time whistle sounded at Appleby Frodingham, the Iron could be proud of their efforts, against a well organised Imps outfit.
Academy manager Tony Daws was full of praise for his academy side, insisting United did have chances to claw themselves back into the game.
"I thought we played well in stages but just lacked that decisive cutting edge in front of goal," he began following the contest on Saturday morning.
"Grayson and even Harvey had chances to give us a foothold in the game but it wasn’t to be and I suppose that’s credit to Lincoln too who defended well throughout."
Facing the Imps once more in the Youth Alliance Cup away next week, the Iron will hope to bounce back with a strong performance away from home.
Daws said: "It’ll be another tough test next weekend, but the boys will be ready for it and it’s all about adapting and learning on this journey. We have to hope they take the positives from today above all."
As mentioned, the Under-18s will face Lincoln City once more away from home next Saturday (11:00 kick-off), in their first EFL Youth Alliance Cup contest of the season.
IRON: Murtagh; Pike, Abraham, Elliot-Bell; Strouther (Stabler, 87) Cribb, Robertson, Hill; Giles; Shillito (Dickinson, 62), Burden-Whittleton.