Shanahan explained that Mitchell re-aggravated his injury during Monday's practice, leading to the decision.
"It's terrible," he said. "I think all you guys know how I feel about Elijah, how our whole team does. Elijah's a stud. He's had some real unfortunate injuries that keep happening, and he had a hamstring injury, and it got worse.
"And the doctor suggested he should have season-ending surgery. I don't know when he's doing that, but that's what he should do, and he's going to do it, and it is unfortunate to not have him for this year."
Another roster move involved activating safety Talanoa Hufanga from the physically unable to perform (PUP) list. Hufanga has been working to return from the ACL injury he sustained in November 2023. Shanahan shared that Hufanga will begin practicing with the team.
"It'll be good to get him in practice today," Shanahan said. "He'll go out with individuals and stuff. We won't throw him in against anybody, but he'll be able to do all the drills and stuff on air with other players and coaches for the first time. And we'll probably do the same thing tomorrow and then evaluate next week.
"I think Tuesday is the first day [we'll decide] whether we want to get him in, going against anyone."
Additionally, Shanahan noted that guard Aaron Banks (finger) is on track to return to practice next week.
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