Bowman posted a photo of himself in a hospital gown on his Instagram account Tuesday morning with the caption, "Time for surgery."
A league source confirmed Bowman's knee is being repaired by renowned surgeon James Andrews in Florida. The 49ers will have a presence there as Bowman begins his rehabilitation.
Bowman suffered the injury while stripping the ball at the goal line in the 49ers' loss to the Seattle Seahawks in the NFC Championship Game. He also suffered damage to his MCL.
Niners coach Jim Harbaugh said on Jan. 21 that Bowman needed two to three weeks before surgery to allow the MCL to heal. Tuesday's surgery represents the short end of that timetable.
The fact that Bowman, one of the best linebackers in the NFL, is having the surgery at this time is vital, because his recovery time is expected to be six to eight months and the 2014 regular season starts in seven months.
The 25-year-old Bowman, a two-time Pro Bowler, recorded 145 tackles, five sacks and two interceptions this past season.