Kelly, 44, had complained of throat pain and was rushed on Tuesday to Northwestern Memorial Hospital, where surgeons the same day drained an abscess on one of his tonsils, spokesman Allan Mayer said.
The Chicago native will be "laid up indefinitely" as he heals, he said.
Last year, the self-proclaimed Pied Piper of R&B released a critically acclaimed retro-soul album, titled "Love Letter," and recently completed the U.S. leg of a worldwide tour. It isn't clear when Kelly might be well enough to resume doing concerts again, Mayer said.
Kelly alluded to discomfort in his throat last week in a tweet, which was also posted on his official website, saying optimistically, "I feel like my throat is coming back. I've been in bed sweating like crazy."
Kelly won a Grammy in 1997 for his gospel-tinged "I Believe I Can Fly," and is also known for his musical melodrama "Trapped in the Closet," a multipart saga about an ever-expanding cast of characters.
The medical issue comes soon after reports that Kelly faces a $2.9 million foreclosure on his suburban Chicago mansion.
Crain's Chicago Business reported that JPMorgan Chase filed a foreclosure lawsuit last month in Cook County Circuit Court. It states Kelly hadn't made monthly mortgage payments since June 2010.
The Olympia Field home's appraised value fell 26 percent in a year, to $3.8 million in 2010, Crain's reported.
Kelly's spokesman has declined to discuss the home but has said the singer is not in financial trouble.