Fowlis, who contributed to the soundtrack of Pixar hit film Brave, won the award for Trad Music in the Media.
It came as the MG Alba Scots Trad Music Awards celebrated its tenth year and was broadcast live on BBC Alba for the first time.
The awards – organised by Hands Up for Trad – saw stars of the scene gather at the Nevis Centre to celebrate and honour the very best of traditional Scottish talent. Other winners included Mike Vass (Composer of the Year), and Paul McKenna (Scots Singer of the Year and Niteworks Up and Coming Artist of the Year).
Fowlis, who could not make the event due to other commitments, said: "I'm delighted to have been honoured with a Scots Trad Music Award. Being part of Disney Pixar's Brave has been a once-in-a-lifetime experience - It has been an incredible opportunity to present Gaelic song to a global audience."
Edinburgh's Scots Fiddle Festival was named Event of the Year, while quirky music venue Bogbain Farm, near Inverness, scooped the prize for Venue of the Year.
Event founder and Hands Up For Trad creative director, Simon Thoumire, said: "It's been a fantastic year for Trad music - We can only hope that successes like these will continue for another 10 years. "