The three-day Long Island Rail Road strike ended with a deal Monday that gave workers a solid raise — but the MTA settled without reforms to notorious work rules officials had sought in exchange for the pay bump.

Throughout the strike, MTA Chair Janno Lieber said he wanted the unions to give up benefits that date back to when the LIRR was privately owned, like a rule that requires double pay for locomotive engineers who drive diesel and electric trains on the same shifts.

The full terms of the deal have not been made public. The contracts still need to be ratified by rank-and-file members of the five unions that went on strike, and must get the MTA board's sign-off. But Lieber on Wednesday acknowledged he didn’t get the work rule reforms he sought.

“We took advantage of the opportunity to make sure that everybody understands how the current system works, that they are outdated, antiquated and somewhat abusive work rules that are still on the books,” Lieber said during a news conference. “Bringing it to public attention and the consequence of public attention, I think is useful from that standpoint.”

The strike came as both sides were hung up on pay raises for the final year of the four-year agreement. A Presidential Emergency Board in March recommended a 4.5% raise for the fourth year, on top of a $3,000 lump-sum payout.

The unions went on to ask for a 5% raise, which MTA officials said would require them to raise fares 8% and possibly impose job and service cuts.

But the MTA ended up giving the workers that 4.5% raise — only stretched out over 14.5 months instead of 12 — as well as the $3,000 bonus, according to spokesperson for the unions, Jamie Horowitz. He said both sides also agreed to transition to modern electronic payroll, which saves money.

“We essentially got a clean deal,” said Michael Sullivan, general chair of the Brotherhood of Railroad Signalmen, one of the five unions involved. “I have to honor the ratification process. I can say I am open to utilizing the 30-day window to meet with the carrier on ancillary items.”

The full scope of the agreement remains undisclosed.

Now that the deal is done, Lieber said he won’t need to raise fares beyond the usual rate of 4% every two years.

The MTA’s budget documents set aside money for a 2% annual pay increase for workers across the agency. Speaking after the contract deal, Lieber admitted there’s flexibility in the budget to accommodate the 4.5% pay raise in the fourth year of the deal — as well as the raises of 3% to 3.5% in the first three years.

“The budget is not a static document. We have a financial plan, there are a lot of variables, but that will allow us to do that without extra fare hikes,” he said, adding riders would not see more than the biannual 4% fare increase. “We're not forcing a much larger fare increase as a result of this agreement.”

Rachael Fauss, senior policy adviser at good government watchdog Reinvent Albany, said it wouldn’t make sense for the MTA to put anything more than a 2% annual pay increase for workers in its planning documents.

“ They put the 2% raise in there because if they put it any higher, they would be negotiating against themselves,” she said. “But I think the reality is that budgets can be political documents, and conservative budgeting can make up a lot of the gaps when unforeseen changes come in.”

The agency ended one contentious bargaining agreement as it embarked on a new one with a much larger union, the Transport Workers Local 100. That union, which represents 38,000 subway and bus workers, is likely to request similar terms to the Long Island Rail Road unions.