San Francisco 49ers

49ers QB Colin Kaepernick has surgery on his thumb and knee

Colin Kaepernick had surgery on his right thumb and left knee in Vail, Colo., on Wednesday, a day after Steadman Clinic doctors determined that the 49ers quarterback needed the arthroscopic procedure on the knee after he had been complaining about pain and swelling for the past few months.

The knee injury occurred in the 49ers’ Nov. 1 loss to the Rams in St. Louis, Kaepernick said this week. Doctors removed “floating bodies” in the joint, drained it and flushed it.

The thumb injury, a partially torn ligament, occurred during an Oct. 22 loss to the Seahawks. He started the following week’s game against the Rams but then was benched for Blaine Gabbert. Kaepernick was sacked 28 times in eight starts after going down 52 times in 2014.

Asked Monday why Kaepernick’s thumb wasn’t repaired after the injury occurred, 49ers general manager Trent Baalke said: “I can’t answer that. I think there’s a process that these players go through. That would be a better question answered by our medical staff.”

Kaepernick was listed on the team’s injury report following the Seahawks game with a hand injury but didn’t appear on the team’s injury report with knee or shoulder issues, both of which resulted in surgery. He was placed on season-ending injured reserve Nov. 21. Kaepernick didn’t miss a practice during his three-season span as the starting quarterback.

He will wear a cast on his hand for six to eight weeks and it is expected to have full strength in three months. Wednesday’s surgeries are in addition to a torn left labrum (shoulder) that Kaepernick had repaired in November at the Steadman Clinic. The shoulder and thumb should be healed at the same time – early to mid April. The knee injury has a much shorter recovery period.

The timing is interesting. Kaepernick will be owed his 2016 salary, the base payment is $11.9 million, on April 1. Because of that cost, the team could trade or cut him before then.

Neither Baalke nor 49ers CEO Jed York said he was concerned about the April 1 deadline, and Baalke has said any talk of cutting or trading the quarterback is premature. He said he and the new 49ers coach – the team will begin interviewing candidates this week – will assess the position together.

“The most important thing is the health of the player and getting him ready for the offseason program,” Baalke said Monday. “I’ve got extreme confidence in our medical staff. I think it’s as good as there is. They’ll continue to work with (Kaepernick). He’s got several things that he’s working through. We’ll get a better grasp of how the rehabs are going and the different things and get him ready for the offseason program. That’s the goal.”

Said York: “I love Colin. He’s been a great piece of this team for a long time. He has certainly helped us get to the level of success that we’ve had. I’m not going to make any decisions on players. A new head coach is going to come in here. He’s going to evaluate the roster. Right now, I want to make sure that Colin gets back healthy.”

Asked if he wanted to return to the team, Kaepernick noted he’s under contract. “I’m doing everything I can to make sure I’m prepared for next season and everything I can do to help this team win,” he said.

The quarterback said he will do some of his rehabilitation work in Vail and some at the 49ers’ facility.

Matt Barrows: @mattbarrows, read more about the team at

Related stories from Sacramento Bee