A youthful side, made up of Under-15s and Under-16s players took on a strong Imps side, with the Iron well in the game for a large chunk of proceedings.
Harrison Poulter added another two goals to his name in the encounter played away from home, as he took his tally to eight goals for the season, with United initially coming from 1-0 down to take a 2-1 lead.
The topsy-turvy first half continued, with Lincoln eventually going in 3-2 up at the break before two further goals were added by the hosts in the second half to complete their victory.
United fell behind after eight minutes when Mekhi Angol struck the first of a brace, before Poulter responded four minutes later to bring the scores level.
Having last netted on August 21st - a brace against Rochdale in the Youth Alliance Cup - Poulter was to emulate that scoring prowess once more, putting Scunthorpe into the lead on 27 minutes.
That lead would last just five minutes though, as Republic of Ireland Under-18 international Billy Brooks scored to make it 2-2.
Oisin Gallagher would put the hosts into the lead four minutes later on 36 minutes when he converted his chance, with the Imps going in at the break 3-2 up.
Eight minutes into the second half, Lincoln doubled their advantage when Finn Abraham put through his own net, before Angol notched his second and Lincoln's fifth 13 minutes from time to add a gloss to the scoreline.
IRON: Balme, Wallace, Burton, Moore, Abraham, Lobley, Cribb, Harris, Poulter, Moore-Billam, Strouther.
IRON UNUSED SUBS: Burden, Burns, Devine, Giles, L Dawson.