The deal is understood to be worth more than £1m, and shows the station still values her despite the show losing 700,000 listeners in the last year.
Radio 1's recent figures showed the station has lost 800,000 listeners over the past 12 months, but Cox still draws 6.9 million listeners a week and last year's figure of 7.6 million was a record high.
The DJ said she was pleased to be staying with the station, adding: "Radio 1 is the best place I have ever worked. The breakfast show means such a lot to me, especially the listeners who I love, so I'm over the moon".
A Radio 1 spokesman added: "Radio 1 is the perfect home for an original talent like Sara Cox so we are really pleased that she has signed to the station for a further three years."
The deal is thought to represent a significant pay rise for Cox, 27, who first got her noticed on Channel 4's The Girlie Show.
The Bolton-born former model took over presenting the breakfast show from her best friend, Zoe Ball, having previously co-presented a Saturday lunchtime Radio 1 slot with Emma B and helped to launch the Sunday Surgery.
She recently filmed a pilot episode of a pop show called Born Sloppy, which producers hope will be commissioned by Channel 4.
But under the terms of her new contract, she is not thought to be making any TV shows for the BBC.