The thumb surgery, which was on his throwing hand, was to repair ligament damage, while the left knee surgery was an arthroscopic procedure to clean out a lingering injury.
Kaepernick will reportedly wear a cast on his thumb for roughly six weeks, and is expected to make a full recovery in three months.
The quarterback also underwent surgery in November on the torn labrum in his left shoulder, from which he will likely be fully recovered in three months, as well.
Kaepernick finished the season with 1,615 passing yards and six touchdowns with a 78.5 passer rating in nine games. He was placed on season-ending injured reserve on Nov. 21.
The 49ers finished the season with a 5–11 record for fourth place in the NFC West Division. Head coach Jim Tomsula was fired by the team on Sunday.