Accused UnitedHealthcare CEO shooter Luigi Mangione stood before a judge in Manhattan for the first time Thursday since allegedly gunning down Brian Thompson in the city, as his attorney griped she was blindsided by the concurrent state and federal charges brought against him.

Mangione entered the courtroom in civilian clothes – a black quarter-zip sweater over a white shirt, tan khakis and orange prison shoes with a “12” on his right foot. He was not wearing handcuffs, but the sound of ankle shackles being removed rang out in the courtroom.

The alleged killer sat calmly between his attorneys as magistrate Judge Katharine Parker read him his rights followed by the charges against him, which include murder through the use of a firearm, two counts of stalking and one count of possession of a firearm.

She asked if he understood what he was being accused of, to which Mangione replied “yes.”

Karen Friedman Agnifilo, Mangione’s lead attorney – who a short time earlier arrived outside Daniel Patrick Moynihan Courthouse relying on crutches to walk – told the court she was blindsided by the new spate of federal charges, saying she’d never encountered anything like it in her career of “over three decades.”

She said she had initially been prepared to go to Manhattan Supreme Court for a hearing at 2 p.m. before Judge Gregory Carro.

“I don’t think they knew this was going to happen,” Agnifilo said, seemingly insinuating that the Manhattan DA’s office didn’t know that the feds were going to have the accused gunman appear today.

She went on to say that Mangione is being charged with two separate crimes, and doesn’t understand how the charges can be so different.

“These seem like two different cases,” Agnifilo said.

“The theory of the murder charge of the Manhattan DA case is terrorism and intimidating a group of people. This is stalking an individual,” she added.

She then asked the judge for some clarity.

“Is there one case, two cases, two investigations? Is there a joint investigation? Frankly, I’ve never seen anything like that and what’s happening here.”

“This is a highly unusual situation that we find ourselves in,” she said, questioning the logistics regarding the parallel state and federal cases. 

In addition to 11 state charges out of New York, the federal rap in connection to the Dec. 4 slaying could make the Ivy Leaguer eligible for the death penalty. Sources tell The Post that the feds pursued their own case in part because New York abolished the death penalty in 2004.

In a statement on the new federal charges, Acting US Attorney Edward Y. Kim for the Southern District of New York hit out at Mangione, calling the killing “a grossly misguided attempt to broadcast [his] views” across the country, adding, “This wasn’t a debate, it was murder.” 

Kim noted that Mangione’s New York trial would likely play out before the federal case.