The Long Island Rail Road awards overtime at nearly double the rate of its sister commuter system, Metro-North — in part because of antiquated pay rules that persist despite having “little to no modern justification,” a scorching new report has found.

The LIRR’s engineering division also has more “high earners” than any other division at the MTA, including the far-larger city subway and bus systems, the study found.

“LIRR has work rules that can double, triple and even quadruple an employee’s income from a single shift,” said the report, which was commissioned by the MTA and released Thursday.

Among the outdated pay-boosting policies is one that gives engineers eight hours of pay for moving an engine at the Sheridan maintenance shop in Queens — even though the task takes just an hour.

Another gives engineers double pay whenever they operate an electric and a diesel locomotive in the same shift — despite the two kinds of trains being nearly identical to operate.

And LIRR employees also score more moolah for tasks that are not among their normal duties, even if they keep their normal schedule.

All told, the LIRR shelled out $225 million in overtime last year.

“The Long Island Rail Road long ago was identified as the problem child of the MTA when it comes to overtime and work rules,” said John Kaehny of good government group Reinvent Albany.

A recent study by the Citizens Budget Commission found the MTA could save $86 million a year if it could just run the LIRR as efficiently as Metro-North.

The commuter railroad’s contract with its major union — Sheet Metal, Air, Rail and Transportation — is up for renegotiation and the MTA has signaled it is seeking major changes.