Francona told Boston's WEEI-AM Ellsbury would "probably" miss the team's stretch run after colliding with Texas Rangers pitcher Tommy Hunter on a play at first base Friday.
"My guess is this may be season-ending," Francona said during his weekly radio show on the station. "I don't know if you rule it out completely, but I don't know if you're going to see him back."
Meanwhile, the Boston Herald reported Wednesday Red Sox outfielder Mike Cameron will have season-ending surgery to fix an abdominal muscle tear, which has bothered him since April.
The newspaper said Cameron will see specialists, then set a time and place for the surgery.