Working for the MTA ­really is a gravy train, with one in seven employees pulling in at least $100,000 a year, according to a new analysis of 2013 salaries.

Nearly 2,500 more workers earned six figures in 2013 than in 2011, the Empire Center for New York State Policy found.

The workers are collecting fat paychecks as riders are about to be socked with 4 percent fare hikes in 2015 and 2017.

“You’re paying these fares, where are they going?” said Tim Hoefer, executive director of the conservative think tank.

“This is a huge chunk of money going to pay salaries.”

The top-earning divisions were the MTA police and LIRR. Most of the six-figure workers reached the benchmark through overtime, the center said.

MTA cops made the most, taking home an average of $125,912 a year. About 85 percent of those officers made more than $100,000 — and that’s before a 7.5 percent pay hike the unionized cops got in January.

LIRR workers did second best, earning an average of more than $83,000 last year. Almost 30 percent earned more than $100,000.

A President Obama-appointed board of negotiators recommended in May a steep 17 percent wage hike over six years for LIRR workers.

But the MTA offered 11 percent, prompting workers to threaten a strike come September.

Metro-North workers didn’t do as well, but still made an average of $78,544 — and 24 percent of employees earned more than $100,000.

Metro-North machinist Eduardo Vargas pulled in a whopping $205,303 in 2013 with overtime — more than tripling his base salary of $61,131.

New York City Transit employees had the smallest percentage of six-figure earners, but 11 percent still made $100,000 or more.

Some of the MTA overtime was boosted by post-Hurricane Sandy repair work.

“In many cases, it is cheaper to pay overtime than hire a new employee,” said MTA spokesman Adam Lisberg. “But in many cases, the distribution of the overtime is controlled not by managers but collective-bargaining agreements [that] assign overtime based on seniority.”

MTA Chairman Thomas Prendergast had the highest pay, making $359,877 in 2013.