The midfielder penned undisclosed terms this morning.
Emery told Arsenal's website: "Joe has progressed a lot in the last year.
"He is technically strong and has shown the confidence to take responsibility and play his game whatever the occasion or opposition.
"I'm looking forward to working with to help him develop further and fulfill his potential."
Emery's faith in Willock has been evidenced by him starting the club's first three Premier League games of this season.
Willock's progression is a "good example" for those still in the academy according to technical director Edu.
He said: "We're delighted that Joe has committed his long-term future to us. The hard work of the academy coaches and staff, Joe, his family and everyone behind the scenes have been key to the development of his potential.
"Bringing young players through to the first team from the academy is an important part of our approach and Joe's progression is a good example for how we want to work in the future.
"Joe has shown hard work and determination to get this far. He's continuing to develop and we look forward to him making a big contribution to the club."