A convincing 6-0 win over Grasshoppers left them 14 points clear of second-placed Mersham, who have a game in hand but cannot now catch the Lilywhites.
The boys are also in the final of the cup after a dramatic extra time win over Mersham a week earlier.
That victory leaves them on course to go for the double when they take on Kennington in the final in early May.
Faversham Town Under 12s head coach Keith Chilvers said the success was down to hard work and team spirit within the squad.
He added: “Good decision-making has also been key, and that will be crucial as the boys move up into the Kent Youth League next season as under 13s.
"This is Faversham Town's youth policy in action. We now have boys in the older age groups competing successfully for first team places, and younger boys pushing ahead to bring success to the club and follow them.”
Keith is now looking to add two or three quality players to strengthen the squad for the Kent Youth League ahead of next season.