A first-half effort from Louis Flower and a Malik Mothersille brace after the break proved the difference at Cobham on Saturday.
The opener came when Alfie Brooks was dispossessed to give Flower a simple finish, but from then until the interval it was Blues asking the questions. George Hall, Callum Sullivan and Jordan James all had attempts as the home side were put on the back foot and left feeling relieved to end the opening 45 still in front.
Chelsea's irritation at being unable to shake off Blues continued when Brooks did well to deny Michael Golding early in the second-half. However, with 65 minutes played the league leaders managed to double their advantage through Mothersille.
The attacker finished well following a check inside before he struck again from a Ronnie Stutter pass in the final ten minutes, with the third goal coming on the back of a spell in which Blues had continued to test Teddy Curd in the home side's goal.
Defeat to the only side with a one hundred per cent record meant Blues were unable to build on their recent success over Tottenham Hotspur in terms of points, but Martyn Olorenshaw was able to identify plenty of positives from the weekend's game.
He told BCFC.com: "We were really pleased on the whole with the performance, we were really dominant. We had 68% possession first-half and a lot was in their half. We were really pleased with how we pressed, we went aggressive and high up the pitch. We were very good at times.
"3-0 sounds like a stroll for them and it was anything but."
The Lead Under-18s Coach went on to outline the learnings from Blues' four matches to date and where they can turn good showings into points.
He said: "We are trying to be as competitive as we can in every game. We have got good players in the group. We are getting stronger in every game and learning around the level. Four games in and we are still learning.
"If we can balance our performance with taking good moments when they come we could have got a different result.
"But there was so much good and so many positives to take from the game. We have to focus on them, tidy things up and hope that in weeks to come we can turn the result our way."
Blues return to action on Saturday as they welcome Manchester United to Wast Hills Training Ground in the Premier League Cup.
Chelsea: Curd; Olise, Wilson, Gee, Silcott-Duberry, Golding (Thomas 61), Castledine (Denny 71), Boniface, Flower (George 86), Stutter, Mothersille.
Unused substitute: Luke Campbell
Scorers Flower 21; Mothersille 65, 83
Blues: Brooks, Sullivan, Oni (Khela 65), Nguepissi, Browne, Ogore, Hall, James, Wakefield, Patterson, Bellingham (Rushton 75)
Unused substitutes: Mayo, Home, Oduka.