Roy, who averaged 21.5 points, needs the surgery to repair a torn meniscus in his right knee.
The three-time All-Star was injured in Portland's 91-88 victory over the Los Angeles Lakers last Sunday. He missed Portland's final two regular-season games.
Roy originally said that he would try to play on the knee for the playoffs. Sixth-seeded Portland plays the third-seeded Suns starting Sunday in Phoenix
"This was not an easy decision to make," Roy said in a statement. "But, if I'm going to be out there, I want to be contributing. If we're fortunate enough to advance in the playoffs, having the surgery now gives me the best opportunity to help our team."
Recovery for such a procedure is typically four to six weeks.
For the Blazers, the announcement erases some of the uncertainty surrounding the playoff series with the Suns.
Roy, who had been told that he could not further injure his knee by playing on it, said earlier this week that he wouldn't return if he was a distraction or a liability.
Roy's injury is the latest to strike the Blazers, who surprised many by even making the playoffs.
Center Greg Oden and Joel Przybilla both sustained injuries that required season-ending surgery. Forward Nicolas Batum missed the first half of the season after shoulder surgery, and swingman Rudy Fernandez had midseason back troubles. Former forward Travis Outlaw, who was traded to the Los Angeles Clippers, sat out for a time with a foot injury.
Roy missed more that a dozen games with a sore hamstring earlier this year before the slight meniscus tear was discovered.
In all, 13 Blazers missed a combined 311 regular-season games because of injuries, second only to the Golden State Warriors this season. Only guard Andre Miller and forward Martell Webster have played in all 82 games.
The latest absence was forward LaMarcus Aldridge, who didn't play against the Warriors after spending the previous night in the hospital with a gastrointestinal virus. He is expected to be recovered by Sunday.
Portland's starting lineup was completely different in the opener than it was for the regular-season finale against Golden State. In all, the Blazers have used 16 different starting lineups.
"At the end of the day you still have to go out and play," Webster said. "We're going to rally together and play the game."
Portland finished the season 50-32, hitting the 50-win mark for the second straight season. The Blazers wound up with the sixth seed in the Western Conference.
Third-seeded Phoenix finished 54-28. The Suns have come on late, going 23-6 since the All-Star break.
The Blazers, who have gone 19-8 since the break, won the season series against the Suns 2-1.
Coach Nate McMillan gave the team a day off on Thursday after losing to the Warriors 122-116 the night before.
"This is a setback, but we've been overcoming injuries all season long," general manager Kevin Pritchard said. "This is about looking long-term and doing what's best for Brandon."
The Blazers made it to the playoffs last season and fell to the Houston Rockets 4-2. With their youth and talent, they were expected to go further this season.
Until all the injuries happened. Now they head into the playoffs as the decided underdog.
"We're not making no excuses," center Marcus Camby said. "There's no excuses if you're going to win the series. So we're coming in confident."
Information from The Associated Press was used in this report.