Regularly scheduled operations on the Long Island Rail Road will resume Sept. 5 after Amtrak’s eight-week track repair project at Penn Station, the MTA said Thursday.

New LIRR timetables reflecting fully restored service will go into effect Sept. 5 — the Tuesday after Labor Day — the Metropolitan Transportation Authority said in a statement. Special bus and ferry service to and from Manhattan will operate for the last time next Friday, Sept. 1.

And discounted fares to alternative stations, including Atlantic Terminal and Hunterspoint Avenue, will be in effect until Thursday, except for weekly tickets, which will be honored through next Friday. Monthly commuter passes for September will return to their regular, full price.

In a statement, MTA chairman Joe Lhota thanked customers “for their patience and willingness to try the temporary travel options” and employees “for their hard work to make the transition as smooth as possible.”

The LIRR has been operating with three fewer tracks at Penn Station since July 8, when Amtrak began an effort to replace some aging track components at the Manhattan transit hub — the busiest in the nation during what Gov. Andrew M. Cuomo predicted would be a ‘‘summer of hell’’ for commuters.

The project required the LIRR to reduce rush-hour service to Penn Station. To mitigate the impact of the service cuts, the MTA has provided several options to customers throughout the summer, including additional trains outside of the rush hour, and buses and ferries to and from Manhattan.

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“Our goal was to provide our customers with a range of alternative travel options and planning tools to limit the repair work’s impact on the daily commute,” Lhota said. “Together, we were all able to get where we needed to go this summer with minimal disruption, and we are pleased that our customers will return from the Labor Day holiday to their regular timetables.”

Penn Station’s other rail providers, NJ Transit and Amtrak, also both announced Thursday their intention to restore normal service at Penn on Sept. 5. NJ Transit executive director Steven Santoro thanked customers Thursday “for their patience and flexibility during the summer months.”

Amtrak modified routes along its Northeast Corridor, which stretches from Boston to Washington, D.C., and diverted some of its Albany trains to Grand Central Terminal throughout the summer work.

Amtrak on Friday will provide its penultimate weekly progress report on the Penn Station repairs. Agency officials have said throughout the summer that the project is running ahead of schedule.

“We thank customers for their patience while we renew the infrastructure at New York Penn Station. We also appreciate the collaboration and support of our commuter partners,” Amtrak co-CEO Charles “Wick” Moorman said in a statement. “Our engineering forces are making great progress and we look forward to resuming scheduled operations Sept. 5.”