Hayden originally rolled his ankle during the first week of organized team activities in late May. An MRI at the time showed no complications but one taken later at the end of minicamp in June showed the stress fracture.
Coach Dennis Allen said Thursday that Hayden could miss up to the first four weeks of camp.
"It's disappointing for him and for me," Allen said. "He's a guy we're talking about being able to step up and help us this year. He's a young player and he needs reps."
It's just the latest setback for Hayden, who has struggled to stay on the field after being drafted 12th overall by Oakland in 2013. The Raiders took a chance on Hayden even though his final year in college at Houston was cut short by a near-fatal heart injury following a practice collision.
After participating in rookie minicamp, Hayden got hurt again during the first full-team practice of the offseason and had to undergo surgery to repair an abdominal scar related to the original surgery.
Hayden didn't get cleared for contact until midway through training camp and never truly caught up. He struggled the first half of the season before he needed season-ending sports hernia surgery in November.
"I think he's frustrated but I don't think he's in a state of despair or anything like that," Allen said. "He has another challenge he has to try to overcome and he understands the challenge ahead of him."
The Raiders had hoped Hayden would start at cornerback across from Tarell Brown. Nickelback Carlos Rogers will now move to the outside on the base defense with rookie TJ Carrie or Chimdi Chekwa playing there in five defensive back situations.
Tight end Nick Kasa (hip flexor) and guard Lucas Nix (knee) also will open camp on the PUP list and not participate in the first practice Friday. Defensive linemen C.J. Wilson (hamstring) and Stacy McGee (thumb) got hurt since minicamp and will be on the non-football injury list.
Safety Usama Young (quadriceps) and cornerback Keith McGill (ankle) were hurt during the conditioning test and will likely open training camp on the PUP list.
The Raiders also will release linebacker Kevin Burnett, who has not been cleared to practice and had lost his starting position after Oakland drafted Khalil Mack in the first round. Mack will play strongside linebacker with Sio Moore and Miles Burris competing for Burnett's spot on the weak side.