Howard missed 22 games this season because of the ankle. He returned in late March and played through pain, but was a big part of Dallas' run to the No. 6 seed in the Western Conference and first-round playoff win against San Antonio.
Howard said Thursday that doctors are "just going in there to clean out all the junk."
He said the surgery will be performed by a doctor recommended by his agent, but that the Mavericks' team doctor agreed with the decision to have surgery.
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The Mavs'season ended Wednesday night, when they were eliminated by Denver in five games.