A criminal complaint accuses Nisreen Assad Ibrahim Bahar, also known as Umm Sayyaf, and her husband of holding Kayla Mueller, 26, captive.
Officials claim she was repeatedly forced to have sex with Abu Bakr al-Baghdadi, the leader of the IS group.
Umm Sayyaf is charged with conspiracy to provide material support to a foreign terror organisation, resulting in death.
The case was filed by federal prosecutors in Alexandria, Virginia, a year after aid worker Ms Mueller was confirmed dead by her family, though it is not clear if or when Umm Sayyaf will be brought to the US to stand trial.
Her husband, Abu Sayyaf, a former IS minister for oil and gas, was killed last May in a Delta Force commando raid on his compound in Syria.
Ms Mueller, from Prescott, Arizona, was taken hostage with her boyfriend Omar Alkhani in August 2013 after leaving a Doctors Without Borders hospital in Aleppo, Syria, where Mr Alkhani had been hired to fix the internet service for the hospital.
Whilst in captivity Ms Mueller wrote a letter to her family expressing her faith in God: "I remember mom always telling me that all in all in the end the only one you really have is God.
"I have come to a place in experience where, in every sense of the word, I have surrendered myself to our creator because literally there was no else and by God and by your prayers I have felt tenderly cradled in freefall.
"I have been shown in darkness, light and have learned that even in prison, one can be free."
Iraqi Umm Sayyaf, 25, who was captured last year, is currently in custody and facing prosecution in her home country.
"We fully support the Iraqi prosecution of Sayyaf and will continue to work with the authorities there to pursue our shared goal of holding Sayyaf accountable for her crimes," assistant attorney general John Carlin, head of the justice department's national security division, said.
"At the same time, these charges reflect that the US justice system remains a powerful tool to bring to bear against those who harm our citizens abroad. We will continue to pursue justice for Kayla and for all American victims of terrorism."
