Tom Prendergast, the Metropolitan Transportation Authority’s chairman and CEO, will retire early this year after a 25-year career with the transit agency, Gov. Andrew Cuomo announced Monday.

Prendergast has led the MTA since June 2013 following terms as president of New York City Transit and the Long Island Rail Road, the nation’s busiest commuter rail system. His term as chairman would have expired in 2021.

His departure was announced a day after the opening of the Second Avenue subway line and comes as the MTA plans other major projects, including the LIRR’s proposed third track along a key stretch of its Main Line.

“It’s never easy to leave an organization after 25 years of service, but I do so knowing that the MTA will continue to serve the public so well and that our governor will ensure New York continues to have the most robust transportation system in the country,” Prendergast said in a statement.

Prendergast agreed to lead the MTA for about three years when Cuomo appointed him, and now has “personal issues and family issues that he needs to deal with,” Cuomo told reporters Monday.

It is uncertain who will replace Prendergast, but Cuomo said he has weeks to find his successor, whom the state Senate must confirm.

“I don’t think you find another Tom Prendergast, but we will be looking for an operator of a transit system who is an operator, also a developer because a lot of what the MTA does is also build,” Cuomo said.

A Chicago native, Prendergast came to the MTA in 1982 as an assistant director of system safety for New York City Transit, which runs the city’s bus and subway systems.

He became the senior vice president for New York City Transit’s subway department before taking the LIRR’s helm in 1994.

Prendergast oversaw the MTA’s Superstorm Sandy recovery, leading repair and fortification projects. He also helped develop the authority’s largest capital program ever, a $27 billion package approved last year that includes a $387 million second track along 18 miles of the LIRR’s Ronkonkoma branch.

In his statement, Prendergast also touted his efforts to implement more technology at the MTA. The agency launched a digital LIRR ticketing program last year.

Cuomo credited Prendergast with the completion of the three-stop Second Avenue Subway, which opened to the public Sunday after more than a half-century of delays.

Larry Penner, a transportation historian and former Federal Transit Administration employee, said Prendergast brought the MTA billions of additional federal dollars and “never promised what he couldn’t deliver.”

To replace Prendergast, Cuomo would be smart to tap an MTA official, such as New York City Transit President Veronique Hakim, who already knows the authority’s inner workings, Penner said.

“The key thing is to bring a native New Yorker who’s already worked for the MTA for a number of years as president of one of the operating agencies so they could hit the ground running,” he said.

Prendergast and Cuomo’s $2 billion third track plan has drawn skepticism and opposition from residents of the 9.8-mile corridor between Floral Park and Hicksville, who say it would disrupt traffic and hurt their quality of life during and after the three- to four-year construction period.

But supporters say it would be an economic engine for Long Island and a great help to commuters, especially after the completion of the long-delayed East Side Access project to extend LIRR service to Grand Central Terminal.

Floral Park Mayor Thomas Tweedy, an opponent of the third track project, said that while he never met Prendergast, he recognized his immense responsibility.

“I don’t doubt that it’s an incredibly time-consuming job and certainly those things the governor has asked him to do, he’s promoted and done what he should,” Tweedy said.

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