Carlos Vicens' team were made to work incredibly hard for the three points, as a resiliant Burnley defence kept City out for much of the game.
The all-important opener finally came with 15 minutes to play as Carlos Borges smashed home at the near post to clinch both victory, and the league title.
The win saw City leapfrog Manchester United on the final day into top spot, clinching the league title by a single point.
The opening stages followed a similar pattern to City's season as a whole, with Vicens' side dominating the majority of the ball.
However, patience was required as a resolute Clarets defence were denying City the chance to bear down on goal.
Our paitence nearly paid off 20 minutes in, as Micah Hamilton tried his luck from 20 yards but his deflected effort flew just wide.
City came even closer two minutes later, as Borges broke in behind for the first time, however his one-on-one effort from close range was well saved by Sam Waller in the Burnley goal.
Vicens' team continued to knock on the door throughout the first 45 minutes and nearly unlocked the solid Clarets back line through the unlikely source of Shea Charles.
The defender joined in with the relentless City attack and fired an effort from 18-yards that was just parried round the post by Waller.
In spite of our dominance the visitors would stand firm to ensure the sides went in at the break all-square.
The second half continued as the first ended, and once again it was Charles who came close.
In similar fashion to his first half chance, the defender hit a fierce, low effort from the edge of the box forcing a good stop out of Clarets keeper, Waller.
Hamilton was the next man to hunt for the all-important opener, as a neat one-two saw him break free into the box. Despite this Waller was once again equal to the effort, saving well at his near post.
City's patience was finally rewarded with just over 15 minutes left on the clock, as we finally found the all-important opener.
Hamilton slotted the ball into Borges who beat his man, before crashing a superb effort in at the near post for his 12th league goal of the season.
Borges' goal would prove the difference and crowned Vicens' side Premier League North champions, on an afternoon to remember for the City youngsters.
HOW WE LINED UP
Oscar Bobb led the line up-front.
WHAT IT MEANS
Victory ensured City were crowned champions of the Under-18 Premier League North division, and sets up a play-off final against either Crystal Palace or Fulham for the national prize.