The Singapore Sports Award was held at the Swissotel The Stamford to honour the nation's top sporting talents for their notable achievements.
16-year-old Schooling, whose achievements in a stellar 2011 included breaking the 200m butterfly SEA Games record and qualifying for the London Olympics in the 200m fly, did not attend the ceremony as he is currently studying in Florida.
Receiving the award on his behalf was his mother May Schooling, who admitted to being nervous although her son was the hot favourite to beat shooter Zhang Jin for the honour.
She said, "I was very nervous the whole day. It would upset him a lot if he didn't win it.
"But now that he has won the award, it will only inspire him to do even better in the pool. This is definitely one of his proudest moments but it will be below his Olympic achievement," she added.
Fu, who won the Republic's first SEA Games women's badminton gold medal last year, admitted she wasn't expecting to beat the likes of Tao Li, Feng Tian Wei and Daphne Tan to the top prize.
The 22-year-old said, "I am delighted to have won the award but surprised at the same time because the other three nominees have done very well too.
"This award definitely means a lot to me and it will motivate me further in my sporting career," she added.
Swimmers made a splash in the other awards as Quah Zheng Wen was named Sportsboy of the Year as the Sportsgirl of the Year award went to Amanda Lim.
Both brought home gold medals at last year's SEA Games, with Quah winning the Men's 400m individual medley while Lim won the Women's 50m freestyle event.
Three new awards were also given out as Terrence Voon from The Straits Times won the "Most Inspiring Sports Story of the Year" while 2011 Formula 1 SingTel Singapore Grand Prix and OCBC Cycle Singapore landed the "Best Sport Event of the Year (International)" and "Best Sport Event of the Year (Local)" awards, respectively.
Sportsman of the Year: Joseph Isaac Schooling (Swimming)
Sportwoman of the Year: Fu Mingtian (Badminton)
Sportsboy of the Year: Quah Zheng Wen (Swimming)
Sportsgirl of the Year: Amanda Lim Xiang Qi (Swimming)
Team of the Year (Event): National Wushu Women's Duilian Team
Sportsboy/Sportsgirl Team of the Year (Event): National Optimist Sailing Team at the World Team Racing Championship
Coach of the Year: William Woo Nam Fatt (Bowling)
Best Sport Event of the Year (International): 2011 Formula 1 SingTel Singapore Grand Prix
Best Sport Event of the Year (Local): OCBC Cycle Singapore
Most Inspiring Sports Story of the Year: "Not just flesh and blood, but the football HEART" by Terrence Voon from The Straits Times