"He made a cut on air," head coach Kyle Shanahan said during a conference with reporters. "It was the last play of practice. Made a cut on air. No one was around him. Just went down. It looked awkward. We're concerned about it, but we don't have an MRI done, so we don't know for sure. So he's going to get that done right now but something with the knee. We'll find out later.
"We're nervous about it, that's for sure."
Shanahan said he is concerned that McKinnon suffered an ACL injury during the practice session. News of the injury was first reported by Matt Barrows of The Athletic.
McKinnon has not played since the 49ers' exhibition opener against the Dallas Cowboys on August 9. He suffered a calf sprain the following Sunday during practice and was not expected to play again until San Francisco's regular-season opener against the Minnesota Vikings.
Saturday was McKinnon's first day participating in 11-on-11 drills following the calf injury, according to Shanahan.
The 49ers signed McKinnon in March to a four-year deal worth up to $30 million. He was supposed to take over as the team's featured running back and was a top priority in free agency.
"It was unusual, the timing of it," Shanahan added. "It was just a couple of hours before the final cuts, and we are extremely concerned, but we don't know for sure until we get an MRI. So he's got to be a part of our 53 and if we get a bad MRI tomorrow, then obviously he'll have to go on IR."
McKinnon entered the NFL in 2014 as a third-round draft pick by the Vikings. He has registered 1,918 yards on 474 carries with seven touchdowns in four NFL seasons. McKinnon has contributed 1,109 rushing yards on 309 carries with five touchdowns over the past two seasons. He also added 94 receptions for 676 yards with four touchdown catches since 2016.
Matt Breida was slated to be McKinnon's primary backup. Breida is also coming back from an injury. He sustained a separated shoulder against the Cowboys on August 9. Shanahan said he is on pace to return as scheduled — for the 49ers' season opener.
San Francisco signed running back Alfred Morris on August 14. The only other running back on the roster after the 53-man roster cut-down is Raheem Mostert.
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