Wendy Sherman, 65, broke the news to staffers yesterday then left on her latest trip for talks with Iran in Switzerland, the paper said.
"It's been two long years," the Times quoted Sherman as saying. Her post is under secretary of state for policy.
It added that, with the departure of Sherman, all the top US officials who have negotiated with Iran over that span will have left President Barack Obama's administration.
Iran and the six global powers leading the talks -- Britain, China, France, Germany, Russia and the United States -- laid down a framework to guide the final accord in eight days of marathon late-night talks in Lausanne in early April.
Kerry and his team will now return to Europe for what is expected to be a final series of meetings with Zarif as the clock ticks down to June 30 and a possible deal putting a nuclear bomb beyond Iran's reach for longer.
