Stanley Tucci has revealed that his co-star will make an appearance in the second film, while he himself will not.
"I know that Hayley is going back to do a flashback scene, but I have not been asked," he told Collider.
Tucci said that he had become close friends with the Black Mirror actress following their work on the 2011 Marvel Studios film.
Atwell has previously been reported to not be returning in her role as Peggy Carter.
Emily VanCamp has been cast in an unconfirmed lead role in the sequel.
Captain America: The Winter Soldier also stars Chris Evans, Sebastian Stan, Anthony Mackie, Frank Grillo, Samuel L Jackson, Cobie Smulders, Scarlett Johansson and Toby Jones and will debut on April 4, 2014.
Watch the trailer for the first Captain America movie below: