Riders get slapped with fare hikes — while these guys ride the gravy train.

The Metropolitan Transportation Authority’s top earner last year raked in a budget-busting $344,147 in overtime — on top of his $117,499 salary, according to data released Tuesday by the Empire Center fiscal-watchdog group.

While delays on the Long Island Rail Road hit a 19-year high in 2018, chief measurement operator Thomas Caputo brought home a fat $461,646 paycheck — more than anyone else at the agency, and $164,027 more than he earned the year before.

And yet the MTA couldn’t even explain how many hours Caputo worked last year, or what his overtime rate was.

“Looking into Caputo,” spokesman Shams Tarek told The Post Tuesday afternoon — then failed to respond to multiple follow-up queries.

After five hours, all he could explain is what a chief measurement operator does — claiming Caputo is “one of only a few people” who can operate an “advanced track-geometry car,” which examines the rails for defects.

Tarek said Caputo retired this month after 30 years on the job — and his hefty final pay year could give a boost to his pension.

The news comes right after the LIRR on Sunday hit riders with fare hikes of up to $15 on monthly tickets and $5.75 on weeklies. Customers say the ­humongous worker paychecks are a slap in the face.

“This is outrageous,” said Dini Morbillo, 56, a physician who spends $275 a month on her LIRR pass and gasped when she heard what Caputo took home.

“He is making more than me — who the hell is Thomas Caputo? Why isn’t there transparency?”

Overtime payments surged to more than $1.3 billion across the entire MTA last year, up from $1.2 billion the year before, according to Empire Center data.

Of that, the LIRR shelled out $224.6 million for overtime, up nearly $50 million from the previous year’s $175.4 million.

And yet that same year, the commuter rail line’s on-time performance dropped to its worst levels in nearly two decades.

Nine of the top 10 overtime earners in the MTA in 2018 worked for the LIRR.

They include surfacing foreman Dallas Bazemore III, who made $279,289 in overtime.

Track worker Marco Pazmino earned a regular salary of just under $55,000, but fattened his pay with another $256,177 in OT.

Meanwhile, New York City Transit chief Andy Byford — the man charged with fixing the Big Apple’s dilapidated subway system — was only the 21st highest earner in the MTA last year, taking home $313,468.

Even LIRR workers were outraged at what some of their colleagues are raking in.

“This guy is making almost $500,000?! Wow. I don’t even know what a chief measurement operator is; all I know is I want in that,” said one customer-service worker, who wouldn’t give his name. “I’m in the wrong department.”

Tarek justified the megasized paychecks by saying the agency has been working on major upgrades recently, and claiming it is often cheaper to pay an existing employee overtime than to hire another person for the same work.

Caputo couldn’t be reached for comment.