A pair of JetBlue pilots raped two female airline workers during a layover in Puerto Rico — and left one of the victims with an STD, a new Brooklyn lawsuit charges.

The heinous incident occurred in San Juan on May 9, after the crew members met Flight Officers Eric Johnson and Dan Watson on the beach and shared some beers after finding out the men were pilots for JetBlue, according to federal court papers.

“The beer was laced with a drug, and after that point, the rest of the night became a blur for [the women],” says the lawsuit, which was filed Monday.

The women — only identified as Jane Doe 1 from Riverton, Utah, Jane Doe 2 from Fort Worth, Texas, and a third crew member with no hometown, ended up back at the Intercontinental Hotel with the pilots, the suit says.

That’s where Jane Doe 1 says Johnson raped her and the third crew member.

“Johnson was on top of [Jane Doe 1] raping her,” the lawsuit says. “[Jane Doe 1] felt the influence of the drug that [Johnson] laced the beer with, and was unable to react to the situation, but was simply aware that it was happening.

“[Her] flashes of memory included Johnson having sexual intercourse with the other crewmember who was also under the influence of the drugs,” according to the lawsuit.

After the assault, Johnson said, “Thank you for making my fantasy come true,” the papers state.

Meanwhile, Jane Doe 2 became sick from the drugs and vomited a number of times, the suit says.

“Johnson and Watson drugged [Jane Doe 2] and intended to rape [her] but did not when [she] began vomiting which was a turnoff,” the suit says.

The next morning, on a flight to Newark, NJ, the women felt “groggy and numb” and “expressed to each other that they were stunned by what had happened.”

The women say they reported the rape to JetBlue but that no action was ever taken against the pilots.

Jane Doe 1 says that Johnson intentionally gave her HPV.

“What happened to my clients is truly horrific, and Jet Blue’s failure to take appropriate action is appalling,” said the women’s lawyer, Abraham Melamed.

The women are suing for at least $75,000 each in damages, plus attorney’s fees and costs.

The pilots could not be reached. JetBlue told The Post that it couldn’t comment on pending litigation. The airline said it takes “allegations of violent or inappropriate behavior very seriously and investigates such claims thoroughly.”