The team says there is no timetable for the All-Star guard's return.
Roy has missed 16 games this season because of soreness in his knees, which he has said is caused by a lack of cartilage.
Roy is averaging 16.6 points in 23 games this season. For his career, the three-time All-Star and 2007 NBA Rookie of the Year is averaging 19.9 points and 4.9 assists.
Roy's decision to have surgery was first reported by the Portland Tribune newspaper on its website. It will be performed next week by Dr. Don Roberts.
"I'm trying to do the best thing I can to get back on the floor," Roy said in a statement Thursday. "We've been able to get a number of different opinions and it's something we've decided."
Last season, Roy had arthroscopic surgery to repair the meniscus in his right knee two days before the Blazers opened their first-round playoff series against Phoenix. He made a remarkable comeback and played in the fourth game of the series, which the Suns eventually won.
In an interview Thursday posted on the team's website, Blazers.com, Roy said he may have been putting strain on his left knee after having the procedure on his right knee.
"The biggest thing, I said in the beginning of this process, I'm going to be patient with it and I'm going to try to think long-term," Roy said. "The team has really backed me with that and hasn't tried to rush me. Just try to be patient with it and try to get me back as close to feeling good as possible."
The team announced on Dec. 30 that Roy would sit out indefinitely this season.
The Blazers have been stung by key injuries. Often-injured center Greg Oden is out for the season after having microfracture knee surgery.
Second-yard forward Jeff Pendergraph also injured his knee and required season-ending surgery. And rookie guard Elliot Williams has undergone surgery this season on both knees.