Several players from the club's youth set-up carried the FIFA and Fair Play banners on to the hallowed Wembley turf before England's World Cup qualifying match against San Marino.
Off the pitch, club chairman Frank Thompson and head of youth development Paul Williams collected the FA award presented by ex-professional players Chris Kamara, Martin Keown and television presenter Ben Shepherd.
"We are incredibly proud of Carshalton Athletic FC, who provide an excellent example of how to run a football club and develop players of all ages and abilities," said Surrey County FA development manager Caroline McRoyall.
"This is a wonderful accolade and something every single person involved with the club should be proud of," said Robins chairman Frank Thompson. "When you consider the number of clubs we were up against throughout the whole of the country, it makes the honour even more special."
Carshalton now go on to compete for the equivalent European title – the UEFA Charter Standard Award – later this year.
It is the third community club award the club has won in 2012, following the South East Regional and Surrey FA achievements. A short video documenting how the club got to where it is currently can be viewed here: http://www.youtube.com/watch?v=5MGt5CZv620
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