The injury occurred in the derby against AIK in early September. Boudri initially tried rehabilitation in the hope of avoiding surgery.
"But he has now felt that the problem with his knee has not completely gone away, and therefore he has decided to have surgery in consultation with our medical team. It is also about what is best for Amin in the long term, and he has many years of football ahead of him," says sports director Mikael Hjelmberg.
Hammarby signed Boudri, a former Gais star, this summer from Los Angeles FC. The transfer has been described as the most expensive in the history of the Swedish league.
The Stockholm club is third in Allsvenskan (Sweden's top football league), eleven points behind league leaders Sirius with seven games left to play.