Baquet, who just last month ascended to the newsroom's top position, informed his staff of the development in an email on Monday morning, according to the newspaper.
After discovering a tumor on his kidney on Thursday, Baquet said he felt it demanded "immediate action." He said he underwent a “minimally invasive, completely successful surgery" on Saturday and his doctors gave him an "excellent" prognosis.
The health scare comes mere weeks after the Times fired former executive editor Jill Abramson in a messy and public split, making Baquet the first African-American to run the paper's newsroom.
“I know this comes as we are all trying to move forward in the newsroom,” Baquet told the staff in his email, adding that he "will be back there as soon as possible.”