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.

Cloth Of Stars, Humphrey Bogart and Red Verdon are the other supplementary entries at a cost of £75,000 each.
Irish trainer Aidan O'Brien has seven of the 18 contenders still in the race, including leading hope US Army Ranger.
The additional entries mean the race will be worth £1.454m and the most valuable ever staged in Britain.
If all 18 horses line up, it will be the largest Derby field for 10 years since the victory of Sir Percy in 2006.
O'Brien, who has won the race five times previously, saddled eight runners in 2007 when his best finisher Eagle Mountain was second to winner Authorized.

The Duke of Rothesay will be joined by newly elected MSPs, diplomats and church leaders at St Giles' Cathedral.
The service traditionally takes place on the evening before the first sitting of a new parliamentary term. This year's ceremony includes a humanist blessing for the first time.
The Prince will meet with Holyrood's party leaders after the service.
The Reverend Calum MacLeod, minister of St Giles' Cathedral will lead the evening service, and Dr Angus Morrison, moderator of the General Assembly of the Church of Scotland, will deliver a sermon.
Guests will be greeted by music from a quartet of the National Youth Jazz Orchestra of Scotland, while musicians from the Royal Conservatoire of Scotland will perform during the service, as will the cathedral's choir.
Departing Presiding Officer Tricia Marwick, who will make a reading during the event, said it would be a "modern" service including representatives of "many faiths".
She said: "It is an honour to take part in a tradition as historic as the Kirking of the Scottish Parliament, a ceremony which was resumed when Parliament reconvened in 1999.
"It will be my pleasure to welcome His Royal Highness the Duke of Rothesay."
Humanist Society Scotland chief executive Gordon MacRae said he was "delighted" that there would be representation for non-religious people at the service for the first time.
He said: "As Scottish society changes it is only fair and proper that representatives from the large group in society that seek to lead ethical and fulfilling lives without religion are included in the country's important ceremonies."
The new session of the Scottish Parliament will formally begin on Thursday, when MSPs will be sworn in by Ms Marwick in the Holyrood chamber.
An election will then be held to choose a new presiding officer, with the formation of a government and the election of a first minister the following week.
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.
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Four horses including joint favourite Wings of Desire have been added as late entries for the Derby at Epsom on Saturday.
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Prince Charles is to attend an interfaith service for the Kirking of the Scottish Parliament in Edinburgh.