Librado Romero/The New York Times

Jay H. Walder, the chairman of the Metropolitan Transportation Authority since 2009, is resigning to take over the MTR Corporation, a transportation company based in Hong Kong, the authority announced on Thursday.

A native New Yorker, Mr. Walder, 52, was selected by Gov. David A. Paterson in July 2009 to run the authority, which operates the city’s bus and subway systems and the Metro-North Railroad and the Long Island Rail Road. He will leave office on Oct. 21, the authority said.

“I believe that we have accomplished quite a lot in a short period, with the support of two governors, the mayor, a hard-working board and many others,” Mr. Walder said in a statement.

His departure was entirely his own decision, according to a person familiar with the matter, who was not authorized to speak publicly. The person described Mr. Walder’s new post as the type of job that he simply could not refuse. The fact that he will remain in office for another three months also seems to indicate that the move was voluntary and that Mr. Walder was not being pushed out.

The MTR Corporation operates a commuter-rail service in Hong Kong as well as intercity rail services between Hong Kong and Beijing, Shanghai and Guangdong. It also runs rail systems in London, Stockholm, and Melbourne, Australia.

Mr. Walder came to the Metropolitan Transportation Authority from London, where he had worked on overhauling that city’s aging mass transit system, to global acclaim.

His relatively brief tenure at the helm of the largest American transit agency has been a bit of a bumpy ride, entailing a fare increase and the prospect of even worse financial conditions on the horizon. He has made real-time information about bus arrivals and up-to-the-minute status reports on the subway lines available to the authority’s beleaguered riders even as the news that those updates bring has been increasingly disheartening, with the authority sustaining its worst service cuts in a generation.

Mr. Walder did not make many friends at Transit Workers Union Local 100, which represents 38,000 bus and subway workers.

“Transit workers won’t miss Jay Walder and quite frankly will be glad to see him go,” said John Samuelsen, the union’s president. “His attempt last year to blackmail the union into major pay and other concessions led to gratuitous layoffs.”

But many officials and transportation advocates praised his work.

“Jay Walder has shown true leadership at the helm of the M.T.A. and been a fiscally responsible manager during these difficult financial times,” Gov. Andrew M. Cuomo said in a statement. “Riders of the M.T.A. are better off today because of Jay’s expertise and the reforms he initiated will benefit all for years to come.”

The head of the clean-transportation advocacy group Transportation Alternatives, Paul Steely White, said in a statement: “Facing a daunting fiscal situation brought on by the governor and state Legislature’s repeated budget raids, Walder kept our trains and buses serving millions of New Yorkers 24 hours every day.”

Mayor Michael R. Bloomberg called Mr. Walder “a first-rate leader with big ideas” who had “made significant improvements to the customer experience,” and said that Mr. Walder’s departure was “a real loss for New York City, the metropolitan region, the state and the country.”

In the name of stability, Mr. Walder’s six-year contract, which currently pays him $350,000 a year and expires in 2015, was designed to give him a big payout if he was removed by one of Mr. Paterson’s successors. Gene Russianoff of the Straphangers Campaign, dean of the transit system’s rider advocates, said that Mr. Walder’s premature departure left the system in a lurch.

“There’s always a learning curve for new management, and this learning curve will occur during the period when they’re fund their incredibly important rebuilding program,” Mr. Russianoff said. “I don’t think it’s so hot.”

Thomas Kaplan contributed reporting.