Mouton suffered the injury to his right knee during practice Thursday.
Mouton was vying to be a rotational player for the Chargers this season.
His short NFL career has been marred by injuries. He was a second-round pick in 2011 but missed his rookie year with a shoulder injury. He played sparingly in just three December games last season.
"Unfortunate news that happened yesterday here, Jonas Mouton tore his ACL," McCoy said. "We'll do the right thing and get him back healthy. ... It's just unfortunate. It's the bad part of the business. You see these players come in here and they work so hard in the offseason. They put a lot of time and effort into it, their entire life to playing the game, and it's an unfortunate thing. You feel so bad for the player."
ESPN NFL Insider Adam Schefter and ESPN.com's Bill Williamson contributed to this report.