Kayla Mueller was abducted when working in Aleppo, Syria and died last year.
The woman charged - 25-year-old Nisreen Assad Ibrahim Bahar, known as Umm Sayyaf -  is currently in Iraqi custody.
Prosecutors say Sayyaf kept Ms Mueller captive, allowing her to be repeatedly raped by IS chief Abu Bakr al-Baghdadi.
Nisreen Bahar's husband, Abu Sayyaf, is described in an affidavit as IS minister for oil and gas, reporting directly to Baghdadi.
Abu Sayyaf died last May when his compound in Syria was raided by US special forces.
His widow was handed over to the Iraqi authorities for prosecution.
A US justice department statement said they supported the prosecution but would "continue to pursue justice for Kayla".
"We will always be relentless in our efforts to identify, locate and arrest those who are responsible for the kidnappings and murders of American citizens," said the FBI's Assistant Director in Charge, Paul Abbate.
Mueller had travelled to Syria as an aid worker when she was kidnapped in 2013.
The widow of a former senior leader in the Islamic State (IS) group has been charged with conspiracy in the death of a US hostage, US authorities said.