The 24-year-old songwriter, real name Victoria Hesketh, came out top in the list, which is compiled by critics, DJs and bloggers.
Hesketh, who was formerly in indie trio Dead Disco, was first spotted and championed by Hot Chip's Joe Goddard.
Other new acts in the list include West London rock act White Lies, fantasy pop duo Empire of the Sun and hip-hop act Kid Cudi.
Last year's list featured acts such as The Ting Tings, Glasvegas, Duffy and winner Adele. Keane, Mika and Corinne Bailey Rae have also won the prize in previous years.
Commenting on her victory in the poll, Hesketh said: "For enough of those pundits to pick me as their favourite act is absolutely incredible and really mind-blowing.
"I'm just so happy that it connects to those people. I hope it goes beyond that and translates and it isn't just some bubble."
The BBC Sound of 2009 Top 10:
1. Little Boots
2. White Lies
3. Florence and the Machine
4. Empire of the Sun
5. La Roux
6. Lady GaGa
7. VV Brown
8. Kid Cudi
9. Passion Pit
10. Dan Black
>Click here to read our interview with Little Boots