Stern -- described by The Washington Post as a key architect of NPR's growth during the past 10 years, had only been in the top job for 17 months when NPR announced he was leaving "by mutual agreement."
NPR's 17-member board -- which features 10 members from member station groups -- declined Thursday to renew Stern's contract, the newspaper said.
Citing sources at NPR, the Post said Stern, 44, had battled often with the board on several fronts, including NPR's expanded use of new media, including podcasting. Some station managers thought the initiatives came at the expense of serving radio stations that pay dues as NPR members.
NPR board Chairman Dennis L. Haaarsager will replace Stern for the time being, the newspaper said, while the board searches for a permanent successor.
Haarsager is general manager of Northwest Public Radio, a 13-station group in Washington state.
"Ken had some really great successes," Haarsager said in an interview. "He did a great job."
However, Haarsager said the board "looked at a lot of things" in deciding not to renew Stern's contract.