Based in the Greater Western Sydney region, the Magic won the inaugural competition after receiving the most online votes for its short video showcasing the club's People, Passion, Health and Happiness.
Giants players Phil Davis and Dylan Shiel were on hand to present the $5000 winner's cheque to the successful club on September 3, which is only in its second year.
Blacktown representative Bradley Whale said the club was excited about taking out the title.
"We have come so far in such a short period of time and to win a national award open to all 3000 AFL community clubs is just great for our club and footy in Western Sydney," said Whale.
"The Swisse Quality Clubs program is a great initiative to help raise the standard of club land. We also had a lot of fun filming our video for the competition."
Swisse ambassador and general manager of AFL NSW/ACT, Tom Harley, also recognised the fledgling club's achievement.
"The Blacktown Magic is one of the foremost emerging clubs in greater western Sydney and it's no surprise that this hard work has translated into being named the 2013 Swisse Quality Club of the Year," said Harley.
"The growth and popularity of Australian rules football in the western Sydney region has shown really strong growth over the past few years, and with community clubs like the Magic developing in the area, players in the west will be able to have a great experience playing our game."
Along with the $5000 cheque for winning the grassroots competition, the Magic also received two tickets to the 2013 AFL Brownlow Medal and the Swisse Ultimate Sportsman's Night.
