The Sabres announced Thompson had the operation on Tuesday and will require five to six months of recovery time. Thompson was initially projected to miss three to five weeks before team doctors determined he required surgery.
The third-year player was hurt in the final minutes of a 4-1 loss at Chicago on Nov. 17. It was Thompson's first NHL game of the season and came shortly after he was promoted from AHL Rochester.
Thompson had seven goals and 12 points in 65 games with Buffalo last season before being demoted to the minors. The 2016 first-round draft pick was acquired by the Sabres in a multiplayer trade that sent center Ryan O'Reilly to St. Louis in July 2018.
O'Reilly went on to lead the Blues to the Stanley Cup last summer. Meanwhile, the Sabres, who haven't made the postseason since 2011, are again on the outside of the Eastern Conference playoff picture. As play began on Tuesday, Buffalo, with 47 points, was seven points away from the last wild-card slot.
The Associated Press contributed to this report.