Rubio has played 22 games this season after spraining his ankle early in the year. He has played only once since March 13 and sat out his 13th consecutive game Saturday night when Minnesota closed out its road schedule against the Golden State Warriors.
The team released a statement before the game that cited ongoing pain in Rubio's ankle as reason for the surgery.
The surgery will be performed by Dr. Richard Ferkel and will take place at the Southern California Orthopedic Institute.
Before playing the Warriors, Minnesota had gone 9-48 without Rubio in the lineup. He missed 42 games earlier this year after injuring his foot.