The 32-year-old Dutchman flew to the United States this week to consult surgeon Richard Steadman, who operated on the same knee in 2000 while the player was at PSV Eindhoven.
After tests and arthroscopic surgery, it was decided to operate again to try to repair damage to the external meniscus, the club said on its website.
"Taking all this into account, the estimated length of absence will be between six and nine months, depending on the clinical development," it added.
Van Nistelrooy damaged the knee during Real's 2-1 Champions League defeat at Juventus last month and missed the Primera Liga matches against Almeria and Athletic Bilbao.
"It's very sad because Ruud is a very important player," striker Gonzalo Higuain said, adding that he hoped it did not spell the end of van Nistelrooy's career.
"We hope he will be back with us as soon as possible because he is a great player and a very good person," he told reporters.
He was Real's top scorer in his first season with 25 league goals and equalled a club record of scoring in seven matches in succession. He netted 16 league goals last season and extended his contract to keep him in Madrid until 2010.
