The Timberwolves announced Thursday the surgery will be done next week in Charlotte, North Carolina, by foot specialist Dr. Robert Anderson. The procedure is called a debridement and repair.
On Monday, coach Flip Saunders announced that Pekovic would be shut down for the rest of the season.
Pekovic played in only 31 games this season, averaging 12.5 points and 7.5 rebounds per contest. The 6-foot-11, 295-pound Montenegrin has missed the past 12 games after sitting out half of November, all of December and most of January with his ankle injury.
Since signing a five-year, $60 million contract with the Wolves in August 2013, Pekovic has played in just 85 games over the past two seasons.