General manager John Lynch informed reporters on Saturday that McKinnon will have another procedure on his knee, which contributed to the decision to place the running back on season-ending injured reserve.
"We sought a lot of opinions on this, and ultimately he decision was made that he needs to undergo another procedure, that he just wasn't going to be ready in eight weeks wasn't going to be an option," Lynch said. "That decision kind of was made for us, and we're hopeful for Jerick that this one is successful. We believe it will be.
"There's a lot of good news about his knee, but unfortunately, there was some mechanical issues that didn't allow him to play this year. That was rough because he worked so diligently to get back, and it was sad to see that not be able to take place.
"But Jerick is a fighter, and he won't be deterred right now. He'll go back on his timeframe, have this done, and then go to work to try to get back and playing football."
The 49ers signed McKinnon to a four-year deal on March 14, 2018, and the running back has not yet made his regular-season debut with the team. He suffered a torn ACL during a light practice on September 1, 2018, ending that season before it started.
McKinnon suffered what was described as a "flare-up" in his knee in July and started training camp on the Active/Physically Unable to Perform (PUP) list. He was activated on August 6 and eased back into practice. A flare-up in his knee sidelined McKinnon after just two practices, and he returned on August 27. One day later, general manager John Lynch revealed that the running back suffered another setback.
The 49ers signed McKinnon with the intention of making him their featured back within head coach Kyle Shanahan's offense. San Francisco has since seen the emergence of running back Matt Breida and signed veteran Tevin Coleman, who played two seasons in Shanahan's offense when the 49ers coach was an offensive coordinator in Atlanta.
The Minnesota Vikings made McKinnon a third-round draft pick out of Georgia Southern in 2014. He carried the football 150 times for 570 yards with three rushing touchdowns while adding 51 receptions for 421 yards with two receiving touchdowns through 16 games and one start with the Vikings in 2017. McKinnon has 1,918 rushing yards on 474 attempts with seven rushing touchdowns through his four NFL seasons played (2014-17).
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