The three activists are accused of using bank accounts in the United States to launder millions of dollars to support Hamas, which the U.S. government has designated as a terrorist organization.
The indictment against the three was unsealed Friday.
The activists include Mousa Mohammed Abu Marzook, whose deputy chief of the Hamas political bureau. Authorities have issued a warrant for his arrest.
The others are Muhammad Hamid Khalil Salah of Chicago and Abdelhaleem Hasan Abdelraziq Ashqar of Alexandria, Virginia. Both men were arrested Thursday night.