Long Islanders might not be the only ones living through a “summer of hell” during Amtrak’s long-delayed track repairs at Penn Station.

Transit advocates fear already troubled outer-borough subway lines will only get worse as the MTA plans to reroute roughly 26 rush-hour Long Island Rail Road trains to Hunterspoint Avenue, Jamaica Station and Atlantic Terminal each day during the Amtrak work, scheduled to span from Monday, July 10, to Friday, Sept. 1.

“It’s pretty clear this is going to put additional strain on the subway system,” said Nick Sifuentes, deputy director at Riders Alliance. “People feel like it’s on the verge of collapse; we’re definitely dealing with overcrowding as it is and the ‘summer of hell’ is only going to make that worse.”

As part of a multifaceted plan involving charter buses and ferry service, the MTA will be incentivizing Long Islanders to make the switch to subways in Brooklyn and Queens, offering fare discounts averaging 25 percent for LIRR passengers traveling to either Hunterspoint Avenue or Atlantic Terminal.

Riders will also get free subway transfers at any of the three hubs, where they can connect to 13 subway lines — the 2, 3, 4, 5, 7, B, D, N, Q, R, E, J and Z.

Those lines average an on-time performance of 56.3 percent, meaning that only that percentage of trains finished their runs within five minutes of their scheduled completion — while also making all scheduled stops. That’s about 8.8 percent below the systemwide average on-time performance of 65.1 percent.

Sifuentes feels some of the planning for the Penn disruptions has focused on the wrong areas. He pointed to Gov. Andrew Cuomo and his call to expedite bridge and tunnel construction to accommodate traffic during the Penn construction as the subway system continued its downward spiral of delays and service outages.

“The lesson learned here is that we need to think about the system regionally and that’s the piece I worry is missing,” Sifuentes said. “It’s that if something goes wrong at Penn or with Amtrak, it impacts the entire system and it impacts how many people are trying to get to subways or [city] buses that barely work.”

Ronnie Hakim, the acting executive director of the MTA, acknowledged that there are rough commutes ahead this summer.

“We know that this is going to be a tough couple of months,” she said during a conference call with reporters on Thursday. But Hakim assured that the agency was taking account for the burden Penn reroutes will have on the subways.

“We are encouraging Long Island Rail Road customers to come to Hunterspoint and jump on the 7 or a Hunterspoint ferry,” Hakim said. “We have coordinated with New York City Transit subway service to be able to know what time those trains are arriving at those different stations, including at Atlantic Terminal, and to measure and provide for adequate subway capacity.”