The victory at Bearsted F.C. was the perfect preparation for the move into the Kent Youth League next season.
The Lilywhites topped their group at the tournament with wins over the hosts, Northfleet Eagles and Hartley De Sales.
A 1-1 draw against Maidstone United in the 15-minute matches meant the boys qualified for the knockout stages unbeaten.
And wins over Vinters Green and Ashford United then put them into a tough final against Thamesview.
And it was the final that was the standout match of the tournament.
Thamesview Under 12s played up a year last season and had gone more than 50 matches unbeaten despite the age difference before narrowly losing an Under 13s cup final shortly before the tournament.
They had romped through their group stages and made short work of their quarter and semi finals.
But it was Town who shocked them with two early goals from Adam Rickard and Paddy Underhill.
Thamesview hit back halfway through the match to make it 2-1 and tried to up the pressure as they hunted for an equaliser.
But they struggled to cope with the pace of the Lilywhites attack and were unable to commit as many players forward as they would have liked.
The boys kept their cool, tackled hard and were able to take the steam out of the match as they saw out the final minutes.
It was their their second trophy in just 14 days.
The boys had already won Ashford United's tournament a fortnight earlier after sweeping aside the hosts 1-0 in the final.
And with skipper George Cutting unavailable for the Bearsted competition, the boys nominated Paddy Underhill to lift the silverware.
Faversham Town coach Brian Flynn said: "Thamesview are the toughest opponents we've come up against for a long time so I'm delighted with the boys' performance.
"We looked a little lethargic in the group matches and didn't play particularly well, but you have to give the boys credit for finding a way to win their games.
"We only started to look sharp in the knockout stages, and saved our best football for the final.
"Our passing game came alive and our tackling was ferocious at times, which is something that has improved massively in the past couple of years.
"To win the tournament against teams of that quality with every single player in the squad playing a major part is a terrific achievement for the boys.
"Thamesview aren't used to losing, and it's easy to see why when you see the quality of their players.
"But they deserve massive credit not only for the way they played, but the way they reacted afterwards.
"They gave our boys a guard of honour and clapped them when they went to collect the trophy, which showed real class.
"They are a credit to themselves and their coach. It's the sort of behaviour you'd like to see from every team, but sadly not all react with such grace and dignity."
The squad now have just one more tournament to play before most head to Sweden to compete in the World Youth Cup in July.
Town squad: George Colyer, Matty Wilton, Alfie Crittenden, Francis Burgess, Noah Pedder, Benedict Bioletti, Ethan Flynn, Callum Bryant, George McIlroy, Paddy Underhill, Samuel Martin, Adam Rickard, Ben Whittington.
Player of the Tournament: Callum Bryant - Always in the thick of the action.