Phoenix, 30, is known for his successful films, including Gladiator, Signs, and The Village.
His agent, Susan Patricola said: "He was uncomfortable with the way he was living his life and found the courage to deal with the disease."
It’s not known at the moment if the treatments will create problems for the filming of his current project, Walk the Line, which is scheduled to begin in June. Pheonix is slated to star in the lead role, playing country singer Johnny Cash.