City were awarded the titles after the Premier League’s Academy Games Programme was determined using a points per game system following its curtailment due to the COVID-19 pandemic.
Players and staff received their trophy and medals in a socially distanced ceremony at the City Football Academy.
The under-18s fine form had seen them establish a 12-point lead at the top of the Northern table before the season ended, but their points per game tally saw them finish the campaign 10.1 points clear of second placed Liverpool.
The young Blues finished the U18 Premier League North Division with a total of 55.6 points, with Fulham winning the Southern Division on 51.8 points.
With the usual national play-off match unable to go ahead, City’s superior tally saw the Club declared as overall champions and Wilcox was pleased to see the youngsters’ efforts rewarded.
The under-18s ended the season with a league and cup double, having also lifted the U18 Premier League Cup in March.
The Academy Director said: "The players and staff should be incredibly proud of their achievements last season.
"They are a fantastic group of young players and winning three trophies in one season is testament to their ability, work ethic and professionalism.
"It has been a fantastic challenge for them considering the team has operated with first year scholars on most occasions.
"We are now looking forward to watching their progress next season in what will be another very exciting and challenging year for them."