The awards, now in their 18th year, honour outstanding achievement at every level of women's sport.
The DH rider star was up against nominees from mainstream sports such as football, cricket and netball.
She received the award from Lord Sebastian Coe, chairman of the 2012 London Olympic Games.
Atherton said: "I was in shock. This was a real surprise. I honestly had no idea that I would win. It is a real honour to be nominated against other such impressive sports women, such high profile sports, so I'm really happy for the sport that we got noticed this way.
"They showed footage of me racing in Fort William and then Lord Coe commented how different I looked all dressed up for the awards and not in my race kit!
"He was really interested in the sport and asked me lots of questions."
Footage of the awards ceremony will be aired on Sky Sports tonight.