The 29-year-old underwent an arthroscopy on his right knee to remove a small fragment, the Eagles said in a statement on Monday.
Kerr will be sidelined from training until mid-to-late January as he spends up to three weeks recovering.
The injury is yet another setback for West Coast, who have been training without All-Australian ruckman Nic Naitanui (groin surgery).
Kerr suffered a serious hamstring injury in 2010 but returned to have a strong season in 2011 and was nearing his best this year.
The 2006 premiership player played 24 games this season as the Eagles reached the semi-final, when they lost to Collingwood by 13 points.Kerr was West Coast's best player against the Magpies in that epic encounter with 29 possessions, of which a whopping 20 were contested.