Iran said on Thursday that accusations that it had targeted former US officials were baseless.
The three men - Masoud Jalili, Seyyed Ali Aghamiri and Yasar Balaghi - were trying to undermine Trump's campaign, Attorney General Merrick Garland told a news conference on Friday.
"We are seeing increasingly aggressive Iranian cyber activity during this election cycle," he said.
The indictment says the three men used fake email accounts to trick several campaign officials into believing they were dealing with a trusted source, and then got them to click on links that allowed the hackers to steal emails and other internal documents, such as debate preparation material and profiles of potential vice presidential candidates.
They then leaked that information to media outlets and the campaign of Biden while he was still a candidate, the indictment said.
Charges include wire fraud, identity theft and computer fraud.
The US Treasury Department also said it was imposing sanctions on the three men along with several other Revolutionary Guard Corps members.
Trump's campaign said in August it had been hacked by Iran but said the perpetrators were not able to get private information.
However, several news outlets have said they declined to publish internal campaign documents that were offered to them.
Biden campaign officials also did not respond when offered Trump's debate preparation material shortly before the two candidates met for their only debate on June 27, the indictment said.
The restraint is a marked contrast to the 2016 election, when hacked communications from Democrat Hillary Clinton's campaign received extensive coverage.
The Iranian hacking team, known as APT42 or Charming Kitten, is known for placing surveillance software on mobile phones that allows them to record calls, steal texts and silently turn on cameras and microphones, researchers say.
The three men are currently in Iran and beyond the reach of US law enforcement but Garland noted that the Justice Department has successfully apprehended other international suspects long after they were charged.
"We will follow these people for the rest of their lives," he said.
