McKinnon suffered the injury about halfway through Sunday's training-camp practice in Santa Clara, California, when he came up grabbing at his right knee. He limped to the side to receive attention from the medical staff and sat out the rest of the session.
McKinnon opened Sunday's practice with a couple of long runs off the right side, but a little later came up gimpy after another play. He hobbled to the side, where the Niners' athletic trainers spent about 10 minutes examining him.
McKinnon pointed to the back of his right knee as he spoke to the medical staff before he eventually stood back up, slapped hands with general manager John Lynch and walked back to join his teammates. He watched the rest of practice and took photos and signed autographs for fans in attendance when it was over.
McKinnon, who signed a four-year, $30 million deal with the 49ers in the offseason, suffered his injury only a few days after backup Matt Breida left Thursday's preseason opener with a separated shoulder. Breida is expected to miss the rest of the preseason but be ready for the regular-season opener Sept. 9 at Minnesota.
Joe Williams, another of the Niners' backup runners, didn't attend Sunday's practice because of a death in his family. After McKinnon departed, Raheem Mostert, Jeremy McNichols and Jeff Wilson were the only three healthy backs available for the rest of Sunday's practice.