The incredible victory in their final league game of 2018 means Barry Lewtas’ side have once again closed the gap on U18s Premier League leaders Everton to just one point.
Duncan gave the Reds the perfect start at Rockcliffe Park when he opened the scoring after just three minutes, but Boro's Stephen Walker converted a penalty soon after to level.
Walker then made it 2-1 before Elijah Dixon-Bonner pounced to equalise, and it was 3-2 to the young Reds by the 27th minute with his second of the match.
Boro's Isaac Fletcher pounced to beat Vitezslav Jaros and level again before the break, before Walker completed his treble with another penalty to give the hosts the lead early in the second period.