The centre-back was operated on by renowned Spanish traumatologist Dr Manuel Leyes at the Olympia Center in Madrid. The procedure was supervised by Real Madrid's medical staff.
The club confirmed the operation in a statement, saying: "Our player Raúl Asencio has been successfully operated on today by Dr Manuel Leyes for a stress fracture in the right tibia. The operation has been supervised by Real Madrid's Medical Services. Asencio will begin his recovery process in the next few days."
Asencio had been managing the injury since January, but a further episode of pain in the affected area this week led to the decision to operate.
The injury is another setback for the 23-year-old, who has yet to feature in an official match for Real Madrid this season.
Asencio initially suffered a muscle injury to the rectus femoris in his right leg on 30 July. He returned to the squad for the match against Rayo Vallecano on 12 September and had been an unused substitute in Real Madrid's following three games.
The option of surgery had already been considered towards the end of last season, with the club and player weighing up whether to use the summer period for his recovery.
Asencio now faces a lengthy rehabilitation before he can return to first-team action. His coach, Jose Mourinho, visited him following the operation.