Federal prosecutors in Manhattan are charging Luigi Mangione, 26, with the federal crime of murder using a firearm, two charges of stalking and a charge of using an illegal gun silencer, according to a criminal complaint.
The complaint accused Mangione of spending months planning an attack driven by his contempt for the health insurance industry and wealthy corporate executives.
Mangione was transferred into the custody of New York City police earlier on Thursday after he waived his right to extradition proceedings at a court hearing in Pennsylvania, the state where he was arrested following a five-day manhunt.
Luigi Mangione's New York defence lawyer Karen Friedman Agnifilo says he has been "overcharged". (AP PHOTO)
According to the federal complaint, a notebook Altoona police found in Mangione's possession contained several handwritten pages that "express hostility towards the health insurance industry and wealthy executives in particular".
A notebook entry dated October 22 described an intent to "wack" the chief executive of an insurance company at its investor conference.
"This investor conference is a true windfall," one entry found in the notebook said, according to the complaint.
"Most importantly - the message becomes self evident."
Police also found a letter in the suspect's possession addressed "To the Feds" that stated: "I wasn't working with anyone," according to the complaint.
"This was fairly trivial: Some elementary social engineering, basic CAD, a lot of patience," the letter said, using an abbreviation for computer-aided design.
Earlier this week, a grand jury in New York indicted Mangione on 11 counts of breaking state law including first-degree murder and murder as an act of terrorism.
Mangione has been in custody since his arrest and has not yet entered a plea.
His New York defence lawyer Karen Friedman Agnifilo has said Mangione has been "overcharged" and that he would fight the charges in court.
Mangione was arrested in Altoona, Pennsylvania, on December 9, five days after Thompson was fatally shot outside a Manhattan hotel before a company conference in what law-enforcement officials have called a pre-meditated assassination.
While the killing of Thompson has been broadly condemned, Mangione has been feted as a folk hero by some in the US who decry the steep costs of healthcare and the power that insurance companies have to deny paying for some medical treatments.
Federal charges potentially allow prosecutors to pursue the death penalty, which has been abolished in New York for decades.
Prosecutors say that Mangione "travelled in interstate commerce" by taking a bus from Atlanta to New York before Thompson's killing and also used his mobile phone and the internet to plan and carry out his attack, and so have jurisdiction.
Mangione is due to make an initial court appearance on the federal charges before US Magistrate Judge Katharine Parker in Manhattan on Thursday afternoon.
"The federal government's reported decision to pile on top of an already overcharged first-degree murder and state terror case is highly unusual and raises serious constitutional and statutory double jeopardy concerns," Mangione's lawyer Friedman Agnifilo said in a statement.
"We are ready to fight these charges in whatever court they are brought."
In Pennsylvania, police said Mangione had a self-assembled 9mm handgun in his backpack and a homemade silencer when he was arrested after being spotted at a McDonald's restaurant.
The handgun resembled the weapon used to kill Thompson, CEO of UnitedHealthcare, the largest US health insurer.
At the Blair County courthouse on Thursday morning, Mangione, appearing in an orange jail jumpsuit, had a preliminary hearing for the Pennsylvania charges, immediately followed by a second on New York's extradition request.
A small crowd of supporters stood outside the courthouse, some waving signs that condemned the health insurance industry.
Mangione spoke only briefly at the extradition hearing, saying he understood his rights and telling Judge David Consiglio he consented to surrender to New York police.