The midfielder was due to see his current deal expire in the summer but Town boss Simon Grayson has moved to tie down his services for at least another season.
The Academy graduate, 20, enjoyed a successful loan spell with Chesterfield this season, scoring five goals in 16 appearances, before firmly breaking into Town's squad at the end of November. He has since enjoyed six outings for the Terriers.
Atkinson told the club's official website: "It is fantastic news - I am over the moon. I have been at the club since I was seven and I am delighted that I am going to be here as it continues to move forward.
"I have learned a lot about the game this season thanks in part to my loan at Chesterfield. I needed to go out and play first-team football to continue my development. My time there has stood me in good stead as I continue to learn about the Championship."
Boss Grayson added: "Chris was given a great opportunity to showcase his ability at the start of the season on loan at Chesterfield and he grabbed it with both hands.
"He played under two managers who both rated him very highly. His time at Chesterfield prepared him for the step up to the Championship and I have been very pleased with his contribution since his return."