The impressive Jadon Sancho scored both goals to secure the three points for the young Blues.
Jason Wilcox made four changes to the side that lost against Chelsea in midweek with Callum Bullock, Marcus Wood, Tom Dele-Bashiru and Sancho coming in for Tosin Adarabioyo, Joel Latibeaudiere, Brahim Diaz and Aaron Nemane.
City started brightly and were dominant in possession in the early stages, something that remained throughout the whole game.
The deadlock was broken in the 18th minute as Sancho scored his third goal for the U18s.
He picked the ball up on the left hand side of the area and bamboozled Matthew Makinson with some brilliant footwork before drilling the ball into the bottom corner.
It was almost 2-0 minutes later when Isaac Buckley saw his glancing header from Jacob Davenport’s free kick saved by Ben Ashcroft.
Blackburn’s only real chance of the game came midway through the first half when Joel Steer found space in the area.
The young Rovers striker thought he had a clear shot on goal before a last ditch tackle from Davenport blocked his effort before Daniel Grimshaw saved the rebounded shot from Mason Fawns.
City continued to apply the pressure on the Blackburn defence and created three further chances before the first half was brought to a close by referee Tom Elliott.
First, Nmecha saw his driven effort somehow tipped onto the crossbar by Ashcroft and then the Blackburn shot stopper denied Buckley from close range.
The flurry of chances continued in the first minute of added time when Ashcroft once again pulled off a good save, this time to deny Davenport as the young Blues headed into half time with a 1-0 lead.
Wilcox’s side started the second half similar to the first with them dominating possession and creating numerous chances.
Ashcroft continued his form from the first 45 minutes by denying Nmecha from ten yards out before Cameron Humphreys saw a hooked effort cleared off the line by Alex Curran.
The waves of attacks carried on following the two early chances as both Buckley and Sancho were denied by Ashcroft.
Nmecha had the ball past the Blackburn ‘keeper in the 67th minute but he saw his effort fly agonisingly past the outside of the post.
The away side continued to soak up the attacks before creating a chance of their own with eight minutes left.
Rovers broke from their own half and the ball was played to Stefan Mols on the edge of the area, who steadied himself before forcing Grimshaw into a save down low to his left to keep his clean sheet intact.
Three minutes of added time were indicated at the end of the second half and City secured the victory in the final minute of the added time.
16-year old Sancho received the ball just inside the area before taking a couple of touches to set himself before burying the ball into the bottom corner to make it 2-0.
Next up for the young Blues is a trip to Finch Farm on Tuesday night as they take on Everton in their penultimate game of the season.
