At least half of Long Island Rail Road workers are earning six-figure salaries — more than any other arm of the MTA, including its own executive headquarters, according to a new watchdog report.

The median pay at the LIRR in 2017 was $104,146 — compared with $90,442 at MTA headquarters and $82,690 at its NYC Transit Authority subsidiary, according to the report from the Citizens Budget Commission released Tuesday.

Meanwhile, the median pay for the MTA’s Metro-North workers was $90,354 — even though the CBC found they’re more productive than their counterparts at the LIRR.

The LIRR uses 10 percent more manpower than the Metro-North lines, based on the number of hours worked versus the hours of operation, the nonprofit group found.

“If the LIRR could match the total productivity of Metro-North, it could have saved the MTA $86 million,” the CBC says.

And riders say the higher salaries at the LIRR sure aren’t resulting in better service — and fares were hiked on April 21.

“It’s bad enough dealing with constant train delays and track problems and all this other stuff,” said Shawn Jemison, 23, who rides the LIRR daily from Bethpage to Penn Station.

“But it’s an extra slap in the face knowing that my money, instead of fixing these problems, is paying high salaries to people who don’t necessarily deserve them.”

Last year, 4,729 of the LIRR’s 7,945 employees took home pay packets of more than $100,000 — as overtime pay at the commuter rail service skyrocketed, according to the Empire Center.

Its highest earner, now-retired chief measurement operator Thomas Caputo, made $461,646 in 2018 — including a whopping $344,147 in overtime pay.

The LIRR paid out $224.6 million in overtime that year, up nearly $50 million from 2017.

The LIRR union contracts are now up for renegotiation — and the CBC notes the last two rounds of collective bargaining at the agency have led to wage increases of 14 percent — with few changes to “work rules” that have allowed workers to rack up seemingly impossible hours of overtime.

One track worker, Marco Paz­mino, logged a staggering 4,157 hours of overtimelast year — the equivalent of working 16 hours a day for all 365 days in the year, factoring in straight time and OT.

© 2019 New York Post