Nearly 10,500 MTA employees were on the six-figure-salary gravy train last year.

More than 14%, or one out of every seven, MTA employees was paid at least $100,000 in 2013, a new report by the Empire Center for New York State Policy found.

“When New Yorkers hear talk about a fare increase, they can check the MTA payroll database to see what they’re paying for,” said Empire Center President E.J. McMahon.

The top MTA earners consisted of upper management, led by Chairman Thomas Prendergast, who had a total cash compensation of $359,877 in 2013.

But the Empire Center’s payroll analysis also found that two-thirds of the $100,000-plus club last year were hourly employees, many of whom boosted their pay with overtime and other payouts.

Eduardo Vargas, a Metro- North railroad machinist, was one of seven who more than tripled their base salary. Vargas, whose salary is $61,131, made $205,303 in 2013.

At $125,912, MTA police employees had the highest average total pay among MTA workers, with 85% paid at least $100,000. And that’s before retroactive and future raises — agreed to this year in a new contract — kick in.

Long Island Rail Road employees, who are threatening to strike unless they get a 17% raise over six years, earned an average pay of $83,794, the highest among the MTA’s operating subsidiaries.

LIRR employees were the largest group in not only the top 100 MTA pay rankings, but also among those who at least doubled their base pay with overtime and other payouts last year.

The report also found that 11% — 5,343 — of workers at the New York City Transit Authority made at least $100,000 last year.

“If people are doing the work, there’s nothing magic about the $100,000 number,” said MTA spokesman Adam Lisberg.

Lisberg said the agency actually has fewer employees than it did in 2009, when the financial crisis hit.