Robert Kiley, the fifth and longest-serving chairman of the Metropolitan Transportation Authority, died Tuesday at his Chilmark, Massachusetts, home from complications of Alzheimer’s disease, relatives said.

Kiley, who led a $16 billion modernization of the region’s transportation network that included building the Long Island Rail Road’s Manhattan rail yard and electrifying the Ronkonkoma branch, was 80.

A former Central Intelligence Agency operative who was tapped in the 1970s by Massachuessetts Gov. Michael Dukakis to head Boston’s transit system, Kiley was appointed chairman of the MTA by Gov. Mario Cuomo in 1983.

The Minneapolis native led the MTA as it carried out its first capital plan — a then-unprecedented $8.5 billion investment in the authority’s infrastructure that was spearheaded by his predecessor, former MTA chairman Richard Ravitch. Kiley led the MTA in passing a second plan that was nearly as big.

Under Kiley’s watch, the MTA upgraded its fleet of subway cars, reduced delays, and grew ridership. Kiley also pushed for improving the quality of commutes, including removing graffiti from subway cars and banning smoking on the LIRR.

“Kiley just took the ball and ran with it and continued the momentum that started with Ravitch,” said Andrew Sparberg, a former LIRR manager under Kiley and author of “From a Nickel to a Token: The Journey from Board of Transportation to MTA.”

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While Kiley was most closely associated with New York’s subway system, Sparberg said his efforts had a lasting impact on Long Island with the electrification of the LIRR’s Main Line as far east as Ronkonkoma and the construction of the John D. Caemmerer West Side Yard. “He certainly should get a positive mark as an important leader of the MTA,” Sparberg said.

In 1990, Kiley also put forth a 20-year wish list for the LIRR that included a connection from Jamaica Station to Kennedy Airport, a rail link to Manhattan’s East Side, and a third track on the LIRR’s Main Line west of Hicksville. One of those efforts — the AirTrain — has since been realized, while the other two are underway.

Not all of Kiley’s LIRR initiatives drew praise. The introduction of “dual-mode” diesel-electric locomotives was plagued with manufacturing delays and reliability problems. And when the railroad fell two years behind schedule and went $100 million over budget in building its Hillside Maintenance Facility, the federal government temporarily cut off aid until the LIRR could prove it could effectively manage capital projects.

“They had all these dreams and ambitions and an empty wallet. And he had to cope with that and advance the projects,” said Gene Russianoff, spokesman for the nonprofit Straphangers Campaign, who praised Kiley for forging ahead with his vision of a cleaner, more reliable transit system even when he was surrounded by doubt and criticism. “Nobody liked rising in a funhouse car covered in paint.”

MTA chairman Thomas Prendergast said Kiley “created a vision that brought the transit system back from the brink of disaster.”

“Bob’s leadership helped the MTA focus on dramatically improving the safety and reliability of the network, led directly to the record ridership levels we see today and was central to the state’s increased growth and prosperity,” Prendergast said.

After leaving the MTA in 1990, Kiley worked in the private sector for a number of years before returning to public transit in 2001 as the head of public transport for London, a job he held for five years.

He is survived by his second wife, Rona, two sons and one granddaughter. His first wife, Patricia, as well as a 2-year-old daughter and 4-year-old son, died in a car crash in 1974.

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A memorial service is planned for October in New York.