With a midnight LIRR strike deadline looming, negotiators for the MTA and unions representing 3,500 workers were racing Friday to try and reach a deal as the unions have vowed to walk off the job if their demands for raises are not met.

Representatives from five unions have said they will strike at 12:01 a.m. Saturday if a contract agreement cannot be reached, threatening the first strike on the nation’s busiest commuter railroad since 1994.

A strike would throw the region’s transit system into disarray, creating headaches for commuters.

Should the sides be unable to find common ground, it is expected LIRR service will some to an immediate halt Saturday morning. MTA officials have said they are prepared to run limited shuttle buses on weekdays, providing service between six locations on Long Island and subway transfer points in Queens.

But the shuttle service is not expected to keep up with the LIRR’s typical ridership of nearly 300,000 people on a weekday.

“There is no substitute for the Long Island Rail Road,” MTA have honchos advised in their strike contingency plan. They recommend that those who can should work from home.

Despite long negotiations on Thursday, sources told the Daily News that neither side seemed to have budged on the issue that has kept them at the table for more than two years: wages.

Both the unions and transit honchos are in agreement on retroactive raises for the rail workers — a 3% pay bump for 2023, 3% for 2024, and 3.5% for 2025. But as the minutes tick down to the unions’ strike deadline, both sides remain at odds over how much the rail workers’ pay should go up in 2026.

The coalition of unions — the Brotherhood of Locomotive Engineers and Trainmen, the International Brotherhood of Electrical Workers, the Brotherhood of Railroad Signalmen, the International Association of Machinists and Aerospace Workers, and the Transportation Communications Union —are demanding a 5% raise, which they say is necessary to keep up with inflation. The MTA, meanwhile, says it’s offering a 3% raise for 2026.

On top of that, the MTA is proposing to add a lump sum payment to account for the difference between a 3% raise and one year of pay at 4.5%. It’s a deal the unions have called a “gimmick,” arguing it will disappear after the contract term, and set them up to negotiate their next contract from a disadvantaged position.

The MTA, for its part, has made clear it does not want to give other, larger unions — the 40,000-strong TWU Local 100, for example, whose subway and bus workers are up for contract renewal this year — ammunition to demand a raise above the typical 3%