US national Joshua Samuel Aaron, 32, was held at New York's JFK airport and will appear in court on Thursday.
He is one of three men accused of illegally accessing the personal information of 100 million people in 2012-15.
Twelve major institutions were victims of the hacking, including JPMorgan.
Mr Aaron had been a fugitive living in Moscow, but flew to the US voluntarily to face the charges, his lawyer said.
In a statement on Wednesday, US Attorney Preet Bharara said: "Joshua Samuel Aaron allegedly worked to hack into the networks of dozens of American companies, ultimately leading to the largest theft of personal information from US financial institutions ever."
The other two suspects are Israeli men: Gery Shalon and Ziv Orenstein. They were arrested in Israel in July 2015, and extradited to the US in June 2016.
All three men were charged in November 2015.
They allegedly manipulated stock prices by selling shares of companies to individuals whose contact information they had stolen.
The men were also charged with running an illegal payment processing business that they used to collect $18m (Â£14.3m) in fees.
Prosecutors claim the men hacked into competitors' systems to spy on them and then hacked into a credit card company investigating their payment processing business in order to avoid detection.
The company hit hardest by the breach was JPMorgan. More than 83 million of the bank's customers had data stolen in the breach.

Based in Doncaster, he simply asked a bunch of strangers: "What do you want?"
With support from the Arts Council England, the results have been put on display in the Frenchgate Centre, Doncaster.
"The project became led by the answers that subjects gave," says Monaghan.
"Political and societal changes have rendered us all as individual consumers, those portrayed have been photographed alone, but when exhibited they are grouped together and their desires for health, happiness and a better world coalesce.
"We want the same things, we want to get along, we want to be social, we want community."
Monaghan also points out that, of the 150 on show, only one wanted a commodity.
Here is a selection of pictures from the project.
You can see more work by Les Monaghan on his blog.

Neil Patterson, 55, of Horsham, West Sussex, was jailed for four-and-a-half months suspended for two years.
Exeter Crown Court heard he repeatedly threatened to kill Samantha Millson.
Charges of assaulting his ex-partner, Katherine Hooper, were dropped after she fell 80ft (24m) from Haytor.
Exeter Crown Court heard that when Ms Millson told Patterson their relationship was over he grabbed a 9in (23cm) kitchen knife and thrust it towards her.
"You and I are going to die tonight," he told her and then stabbed the knife into his leg and withdrew it covered in blood.
The court heard from a probation worker that Patterson was deemed to be "low risk".
But Jacinta Wainwright of domestic abuse charity Stop Abuse For Everyone told the court: "I find it extremely concerning that the view is that someone who would use a knife as a weapon and threaten to harm them is low risk.
"It's well known that when someone is behaving in that way it's a very high risk situation."
Three years ago Patterson faced an assault charge against his then partner Katherine Hooper, 24, which he denied.
Ms Hooper later jumped off Haytor on Dartmoor with the couple's eldest son Joshua on her back. A coroner said she took her own life.
Both died and charges against Patterson were dropped by prosecutors.
Former Det Sgt Andy James, who led the investigation into the deaths, said: "It's an opportunity lost. The accused should go there and face that accuser and if for whatever reason that is thwarted that is disappointing.
"I would have liked to have seen Kat in court. I think she would have been robust, honest and truthful."
Patterson was also handed a restraining order protecting Ms Millson.
FBI and US secret service agents have arrested a man charged with the largest cyber-attack of financial firms in America's history.
[NEXT_CONCEPT]
There are times when it is best to keep things simple, and that's just what Les Monaghan has done for The Desire Project.
[NEXT_CONCEPT]
The ex-partner of a mother who jumped to her death from a Dartmoor tor with her five-year-old son has been spared jail after admitting threatening a subsequent girlfriend with a knife.