He’s found a way to make your commute even worse.

A subway saboteur has been terrorizing the city’s underground during peak hours by climbing into the backs of trains, yanking the emergency brakes — and then vanishing into the tunnels, officials said Wednesday.

The transit fiend struck as recently as Tuesday night along the northbound 2/3 line — but may have been pulling the stupid stunt for “years,” MTA boss Pat Foye said.

“We believe there is an individual or a group of individuals who are systematically gaining access to subway cars, pulling the emergency brakes and then fleeing to the tracks, getting on the next train and then repeating the process,” Foye said during the agency’s Wednesday board meeting. “This is not an isolated incident and may have been happening for several years.”

Officials say they’ re still trying to nail down if it’s just one scofflaw or a whole gang and how long it has been going on.

The “morons” — or moron — appears to have a master key to the employee-only cabin at the end of each train, subway chief Andy Byford said.

Investigators believe he is hopping onto the backs of trains — mostly 2 and 5 trains — unlatching security chains and then using the key to gain access to the cabin, Byford added.

He then yanks an emergency-brake lever, grinding the train to a halt before scampering off into the darkness. “It’s stupid, it’s dangerous, it’s selfish and it’s got to stop. We’re going to hunt them down. We intend to nail them,” Byford said.

The NYPD, meanwhile, announced it is deploying 25 extra cops to scan the subways in hopes of catching whoever is responsible and that reckless-endangerment charges are likely.

The MTA couldn’t provide a number of incidents so far but said many took place in between stations while trains were in motion.

Incident reports provided by a source show at least four incidents in May with the same M.O. — the brake is pulled and when a conductor comes to investigate, they find the “storm door” is open and the safety chains are down.

Two of those incidents happened within two minutes of one another at the Winthrop Street Station in Brooklyn.

Foye said the MTA had been reluctant to speak out about the events “given the potential for copycats” — but officials are now seeking the public’s help.

The issue first came to light Tuesday when the MTA tweeted that “someone has intentionally disrupted thousands of commutes on the 2/3 lines today by activating multiple trains’ emergency brakes.”

Straphangers were furious to learn of the scofflaw sabotaging their rides home. “It’s already hard enough to get home at night,” said one giving only his first name David, 30.

Additional reporting by Lia Eustachewich