The drug company CEO who ignited outrage by raising the price of an AIDS and cancer medication by 5,000 percent was hauled out of his luxury Murray Hill apartment in handcuffs on Thursday and charged in an alleged $11 million Ponzi scheme.

Martin Shkreli, 32, who hiked the price of the lifesaving prescription drug Daraprim from $13.50 a pill to $750, was hit with securities-fraud and conspiracy charges in the unrelated case in Brooklyn federal court.

A conviction could put him in prison for 20 years.

“The charges announced today describe a securities-fraud trifecta of lies, deceit and greed,” said FBI Assistant Director in Charge Diego Rodriguez, who announced the case along with US Attorney Robert Capers.

The millionaire Sheepshead Bay native — who boasted of owning a Picasso and dropped $2 million on a one-of-a-kind Wu-Tang Clan album — was hauled out of his apartment in a gray hoodie.

Asked in court whether he understood the charges, Shkreli seemed nervous but composed as he told Judge Robert Levy, “Yes, your honor.”

His brother and father watched at his side, allowed into the courtroom well after they agreed to guarantee Shkreli’s $5 million bail.

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Shkreli pleaded not guilty through his lawyer and was released immediately, paying his bail from what prosecutors deemed an untainted account.

The feds did not move to seize any of Shkreli’s assets, meaning he got to keep his Wu-Tang album, “Once Upon a Time in Shaolin.”

The scrawny, baby-faced entrepreneur donned dark Ray-Ban glasses before walking out of court to an SUV. A guard led him through a crowd of journalists.

Shkreli created his Ponzi scheme as he paid off debts from two failing hedge funds by tapping assets from his biopharmaceutical firm, Retrophin, the feds said.

In all, he is accused of misappropriating $11 million for that scheme and for personal expenses.

With his hedge funds foundering due to bad trades, Shkreli looted Retrophin between 2009 and 2014 to keep up the illusion of solvency, the feds said.

When regulators started probing the money maneuvers, Shkreli and an attorney, co-defendant Evan Greebel, tried to conceal their actions, the feds charged.

He “engaged in multiple schemes to ensnare investors through a web of lies and deceit,” officials said in a statement.

Shkreli told one investor that his hedge fund held $35 million in assets, even though it had only $700, the charges alleged.

After he was freed Thursday, a rep for Shkreli said he was “confident he will be cleared” and blamed the charges on his infamy over the Daraprim price-gouging.

“It is no coincidence that these charges, the result of investigations which have been languishing for a considerable period of time, have been filed at the same time of Shkreli’s high-profile, controversial and yet unrelated activities,” the rep said.

Shkreli was widely reviled last year when his other drug company, Turing Pharmaceuticals, bought Daraprim and, in September, dramatically raised the price.

It is the only approved drug for toxoplasmosis, a rare parasitic disease that hits pregnant women and people with AIDS and cancer.

The hike was condemned by public figures as disparate as Hillary Clinton and Donald Trump, who called him “a spoiled brat.”

Additional reporting by Melkorka Licea and Post wire services