He is going to be CEO beginning November 12, a New York Times spokesman said on Sunday.
The New York Times maintained its confidence in the paper's new chief following the news that George Entwistle, the director-general of the BBC, said he was resigning from the broadcaster on Saturday. Entwistle took the blame for a news program at its flagship Newsnight, which aired a mistaken allegation that a former British senior politician sexually abused children.
The latest embarrassment comes as the BBC faces police and other investigations into claims that hundreds of people, some as young as 12, were sexually abused over the course of decades by one of their top personalities, the late Jimmy Savile. It is also facing awkward questions over how the same Newsnight program - while Thompson was director-general - killed a report that was investigating complaints against Savile
and instead aired laudatory shows commemorating Savile after he died last year.
Thompson said he did not know about the nature of the investigation by Newsnight into Savile, and had no involvement in the decision to axe the report.
He later said he had a chance meeting with a journalist who mentioned the Newsnight investigation into Savile, but said he had not been told any of the details or the scale of the problem.
Entwistle's departure and his acceptance of responsibility for editorial decisions as director -general, adds pressure to any evaluation of Thompson's role at the BBC and whether he was ultimately accountable for the shelving of the Savile report.
Thompson did not immediately respond to a request for comment regarding Entwistle's resignation. Earlier, he declined to be interviewed about his plans for the New York Times.