WASHINGTON — President Obama’s chief negotiator with Iran, Wendy R. Sherman, said on Wednesday that she planned to leave the administration shortly after the June 30 deadline for a final deal on limiting the country’s nuclear program.

“It’s been two long years,” Ms. Sherman, the under secretary of state for policy, said in her office on Wednesday. With her departure, all the top officials who have negotiated with Iran over those two years will have left the administration, leaving questions about who will coordinate the complex process of carrying out a deal if one is struck by the deadline.

On Wednesday night, Secretary of State John Kerry, who has relied on Ms. Sherman to conduct the high-stakes negotiations, said that her “mentoring of colleagues, her experience, her passion for diplomacy, her calm in the storm set her apart as a great under secretary of state.”

Her predecessor, William J. Burns, a key player in the secret diplomacy with Iran in 2013 that ultimately led to formal negotiations, recalled that “there were many moments when our own government, and our negotiating partners, were on different paths with the Iranians, and she was the one who always made sure there were no gaps.”

Her work is hardly done: Ms. Sherman left for Austria and Switzerland on Wednesday, shortly after telling her staff about her plans, on her 30th trip as lead negotiator. Over the next five weeks, her task will be to see if the final

differences with Tehran — on issues like the timing of the dismantlement of much of its nuclear infrastructure and the details of inspections of military and other sites — can be bridged.

It will be a familiar rhythm for Ms. Sherman, 65, a wiry, intense negotiator with short-cropped white hair who stood out in photographs of the talks in a room dominated by men. (Her colleagues had T-shirts printed with the words “Team Silver Fox.”)

She has often compared the negotiations to a Rubik’s cube, because they involve lining up so many interrelated elements. “It’s incredibly complex,” she said Wednesday, “with the Congress, with the press, our negotiating partners — and then, when you are done with that, negotiating with the Iranians. And because we’re in the world of 24/7, if there was ever a time when you could aim a message to one audience and hope it was kept from another audience — well, that’s not possible, if it ever was.”

Mr. Obama, who hopes that a deal will be among his biggest foreign policy legacies, said in a statement that he had “long counted on Wendy’s unique combination of intellect, toughness and persistence, which have made her one of the most effective diplomats of her generation.”

But many Republicans in Congress view her as the architect of a plan that was intended to avoid any direct congressional vote on an ultimate deal. Until a movement on Capitol Hill in April, the administration did not plan to put an accord — which would be a political agreement, not a treaty — to a vote until Congress had to permanently revoke sanctions against Iran, perhaps years from now. Instead, under legislation that Mr. Obama signed last week, Congress will now vote on a final accord within a month or two of any agreement. Even if Congress rejects it, Mr. Obama’s chances of prevailing seem high, since Republicans would not have the votes to override a veto.

Ms. Sherman, the No. 3 official at the State Department, said she did not expect to take another post in the administration, and she has not announced any plans. But she is close to Hillary Rodham Clinton, whose presidential campaign she supported in 2008, and who is running again for the Democratic nomination.

It was Mrs. Clinton who brought Ms. Sherman back into the government to handle Iran and other issues. Previously, she had worked as a social worker in Boston, a Senate campaign aide, and a counselor to Secretary of State Madeleine K. Albright during the Clinton administration, handling North Korea. Her congressional critics often cited that credential in critiquing her negotiations with Iran.

“The American people need an insurance policy to prevent a rerun of North Korea,” Senator Mark S. Kirk, Republican of Illinois, said last year.

The Iran agreement is far more detailed than any of the failed accords reached with North Korea, but that is no guarantee of success. Administration officials are concerned that with the departures of Ms. Sherman, Mr. Burns and Jake Sullivan, one of Mrs. Clinton’s top aides, much of the historical memory about the Iran deal could be lost.

Ms. Sherman said that the larger question of the Iran talks — whether they could lead to a broader rapprochement between two countries that have been bitter adversaries for 35 years — would take years to play out.

“We don’t know the end of this story,” she said. But when she comes home in frustration over the back-and-forth of the talks, she said, her husband, Bruce Stokes, a longtime Washington journalist, “reminds me that this is historic.”

This article was written by David E. Sanger for The New York Times on May 27, 2015. David E. Sanger is chief Washington correspondent of The New York Times.  Mr. Sanger has reported from New York, Tokyo and Washington, covering a wide variety of issues surrounding foreign policy, globalization, nuclear proliferation and Asian affairs.