Mitchell suffered a sprained MCL in his right knee in Sunday's 19-10 loss to the Chicago Bears. He departed the game with about 10 minutes left in the second quarter, and a return was ruled out just before halftime.
"We're estimating about two months, eight weeks, give or take a few," Shanahan said. "So, hopefully, it goes well and it's earlier but you never know with those things, so that's what we're guessing."
After Mitchell was ruled out, it wasn't clear how he was hurt, but Shanahan said Monday that the running back suffered the injury on an 11-yard run off left tackle with 12:54 left in the second quarter. Replays show Bears safety Eddie Jackson diving to make the tackle on Mitchell and colliding with his knee just as Mitchell is planting his foot in the ground.
Mitchell stayed in the game for a few more plays and helped block for receiver Deebo Samuel's 6-yard touchdown with 10:11 to go in the half. Samuel's touchdown was Mitchell's last play before he was ruled out because of the knee injury.
It was the latest in a series of ailments that have slowed Mitchell's young career. In 2021, Mitchell set a franchise record for rookie rushing yards (963) and added five touchdowns despite missing six games with rib, knee, finger, shoulder and head injuries.
In the offseason, Mitchell added a few extra pounds in hopes it would help him handle the pounding an NFL running back endures. Shanahan believed Mitchell, who had six carries for 41 yards before the injury, was positioned for a big season.
"He was pretty down," Shanahan said. "For obvious reasons, we're down for him. Elijah went through a lot last year, it's well documented the injuries he had. He really worked hard this offseason. He was feeling really good going into that game and man, I thought he looked really good before he got hurt.
"And just unfortunate hit that he had. I just tried to tell him to keep his head up. Anybody who would have gotten caught in that situation would have gotten hurt with the way his foot planted in the ground and the guy hit his knee. I think we were just real fortunate it wasn't worse."
Mitchell is slated to go on injured reserve this week, creating a roster spot for the 49ers. For now, they have the trio of veteran Jeff Wilson Jr. and rookies Jordan Mason and Tyrion Davis-Price on the 53-man roster. Wilson and Samuel got the bulk of the running back carries after Mitchell left Sunday's game.
Wilson figures to get the first crack at replacing Mitchell, but Shanahan said the untested rookies will be asked to contribute as well.
"They're two talented players who we think can help us a lot running the ball," Shanahan said. "But they've got to grow up fast."