Representative Allan Mayer said Thursday that the 44-year-old left Northwestern Memorial Hospital in Chicago and is recuperating at his home in the city.
Mayer said it was not clear when Kelly would be well enough to continue performing.
The Grammy-winning singer had complained of throat pain and was taken to the hospital on Tuesday. The same day, surgeons drained an abscess on one of his tonsils.
Kelly released a critically acclaimed retro-soul album last year, titled "Love Letter." He recently completed the U.S. leg of a worldwide tour.
Kelly won a Grammy in 1997 for his gospel-tinged "I Believe I Can Fly."
The Associated Press contributed to this report.