Hoda Muthana said she was "really young and ignorant" when she joined IS and now wishes to return home.
The former wife of Australian IS fighter Suhan Rahman, who was killed in 2015, will not be allowed to return to the US.
Hoda Muthana left Alabama to join IS when she was 19, and this week pleaded with authorities to let her come home.
The United States announced it would refuse to take back the US-born woman, saying that she is no longer a citizen.
"Ms Hoda Muthana is not a US citizen and will not be admitted into the United States," Secretary of State Mike Pompeo said in a statement.
"She does not have any legal basis, no valid US passport, no right to a passport, nor any visa to travel to the United States.
"We continue to strongly advise all US citizens not to travel to Syria."
US President Donald Trump said on Twitter he has "instructed" Mr Pompeo "not to allow Hoda Muthana back into the country" - a break with usual US protocol not to comment on individuals' immigration issues.
Mr Pompeo's statement on the Alabama native - one of the few Americans among the hundreds of Europeans to have joined the ranks of the Islamic State group in Syria - is at stark odds with his calls on other countries to bring back and prosecute their own jihadist nationals.
The decision also sets a serious precedent and possible legal challenges as it's generally difficult to lose US citizenship.
Muthana was born in the United States to parents from Yemen who became American citizens, according to the Counter Extremism Project at George Washington University.
The 24-year-old said in an interview with The Guardian that she had been brainwashed online and "deeply regrets" voluntarily joining the movement.
"I believe that America gives second chances. I want to return and I'll never come back to the Middle East," she said.
Her lawyer Hassan Shilby refuted the government claims, saying Ms Muthana "is a US citizen" She has a valid passport".
Ms Muthana left her Alabama home in November 2014, travelling to join IS in Syria. Shortly after her arrival, she agreed to marry Rahman, known as Abu Jihad Al-Australi, who was originally from Roxburgh Park in Melbourne.
But three months later, Muthana reportedly announced his death on Twitter alongside an image of him lying on the ground covered in blood.
“May Allah accept my husband, Abu Jihad al Australi. Promised Allah and fought in the front lines until he obtained shahadah,”she wrote.
In social media posts before his death, Rahman had urged Australians to “let the heads fly and blood flow".
"Spill blood young aussies. Don’t be humiliated especially if u cant b here in sham [Syria]," he wrote.
In late 2014, shortly after moving to Syria, Muthana posted on Twitter a picture of four women who appeared to torch their Western passports, including an American one.
Earlier, State Department deputy spokesman Robert Palladino declined to discuss Muthana's case specifically, said that the status of US citizens detained in Syria "is by definition extremely complicated".
Hassan Shibly, a lawyer for Muthana, said it was disappointing that US officials had not interviewed her.
"It's really problematic that The [New York] Times, The Guardian and ABC News have all been able to meet with her and interview her, and the government has not been able to do that," Mr Shibly said.
The situation of foreign jihadists detained by US-allied Kurdish forces has taken a new urgency as US President Donald Trump plans to withdraw US troops from Syria.
The US has also recently urged European powers to take back hundreds of their citizens who fought with the Islamic State movement in Syria, but acknowledged the situation was complex in the rare case of an American jihadist.
Mr Trump has contemplated reopening the US military base at Guantanamo Bay to take in new foreign inmates, while Britain on Wednesday revoked the citizenship of a female jihadist who wanted to return home with her newborn baby.
Neither option would likely pass muster in the cases of US citizens, who enjoy strong legal protections under the Constitution.
Muthana, who married two more jihadists after the death of Rahman and has a son with one of her husbands, had previously took to Twitter to urge attacks on fellow Americans.
In the interview, Muthana, who is living in a Syrian refugee camp, said that she was "really young and ignorant" when she joined IS and has since renounced radicalism.
“It’s been a difficult journey for her, and she's relieved. She's very resentful to them for having misguided her and having brainwashed her and manipulated her and really destroying her life,” Mr Shibly said.