Bulger was on the FBI's Ten Most Wanted fugitives list in 1999, and was considered the most wanted person in the list behind former al-Qaeda leader Osama bin Laden.
"Three men have been indicted in connection with the beating death of James 'Whitey' Bulger," the Justice Department said on Thursday.
Fotios Geas, Paul DeCologero, and Sean McKinnon were charged this week with conspiracy to comment first degree murder, the release said.
Geas and DeCologero are accused of beating the 89-year-old Bulger on the head multiple times, fatally wounding him, in October 2018, the release said. The incident happened when they were in prison at the US Penitentiary Hazleton in the state of West Virginia, the release added.
The three men are currently in the custody of authorities, the release said.