The whistleblower behind the Massachusetts Institute of Technology’s Jeffrey Epstein donation scandal said her “job was to protect secrets” — and recalled how female staffers mocked him as “Voldemort.”

Signe Swenson blew the lid on her ex-boss, Joichi Ito, the ousted director of MIT’s prestigious Media Lab, providing emails to the New Yorker that showed Ito’s relationship with Epstein was far cozier than he let on.

“I felt like it was my job to protect secrets,” Swenson told the Guardian in an interview Thursday.

Soon into her gig as a development associate and alumni coordinator at the Media Lab, Swenson said, she was told her responsibilities would include helping “the existing relationship between Joi Ito and Jeffrey Epstein along.”

Three months later, however, she was told to “wipe every trace of Epstein from the university’s record.”

“I realized that the job was never going to be what I wanted it to be,” Swenson said.

Ito — who resigned from his position at the lab last week — initially claimed Epstein only donated $525,000 to the research center, but the bombshell emails revealed the dead pedophile actually gifted at least $7.5 million.

Swenson recalled one time when Epstein — who had been marked as “disqualified” in the school’s donor database — made a small donation of “50 or a hundred thousand dollars” to help restore a Rothko painting. Months later, he issued a press release touting the donation.

“We were all frantic,” Swenson said. “The MIT press office reached out to investigate. They were wanting to refute or play down what he’d said. If it came out, Joi was ready to call Epstein to ask him to take it down.”

It turned out the press release gained little traction. But it was clear, as Swenson said, that Epstein was “showing Joi that he had to keep him happy.”

“He was saying to Joi, ‘I can destroy you by telling people you know me,'” she added.

Swenson, who quit her job at the lab after three years, slammed her former boss’ claim that he never witnessed anything untoward during his time with Epstein. She called it “implausible.”

Ito traveled to the financier’s homes in New York, the US Virgin Islands and Mexico, and even once turned up at the lab with him and two Eastern European “assistants,” she said.

“I don’t want to think about the worst,” Swenson said. “Joi spent time in Epstein’s homes and regularly socialized with him. It felt like bringing these two women everywhere, especially to scientific meetings, was a distraction. And the idea that they thought nothing was underfoot is impossible to believe.”

The former lab worker also said women in the office — who nicknamed the multimillionaire “Voldemort” after the evil character in Harry Potter — were wary of the Ito-Epstein connection.

“[A] small group of women in the office realized this was wrong, that this should not be happening, and that Epstein should not be running around MIT,” she said.