The Trump administration's refusal to admit 24-year-old Hoda Muthana could set precedent and face legal challenges as it is generally extremely difficult to lose US citizenship.
"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 terse 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," he said.
"We continue to strongly advise all US citizens not to travel to Syria," he said.
Pompeo did not elaborate on the legal rationale for why the Alabama native, who is believed to have travelled to Syria on her US passport, was not considered a citizen or where she should go instead.
Pompeo's statement on Muthana - one of the comparatively few US-born jihadists amid 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.
Just this weekend, President Donald Trump took to Twitter to chastise European allies who have not taken back Islamic State prisoners caught in Syria.
US-born and radicalised
Muthana was born in the United States to parents from Yemen who became naturalized American citizens, according to the Counter Extremism Project at George Washington University, which has identified 64 Americans who went to join the Islamic State group in Syria or Iraq.
In late 2014, shortly after moving to Syria, Muthana posted on Twitter a picture of herself and three other women who appeared to torch their Western passports, including an American one.
She went on to write vivid calls over social media to kill Americans, glorifying the ruthless extremist group that for a time ruled vast swathes of Syria and Iraq.
But with the Islamic State group down to its last stretch of land, Muthana has said she has renounced extremism and wants to return home.
Muthana, who has been detained by US-allied Kurdish fighters, said that she had been brainwashed by reading social media as a closeted teenager in Hoover, Alabama.
"To say that I regret my past words, any pain that I caused my family and any concerns I would cause my country would be hard for me to really express properly," she said in a note to her lawyer reported by The New York Times.
She was married three times to male jihadists and has a toddler son.
Tough to lose US citizenship
The US decision on Muthana comes amid rising debate in Europe on the nationality of extremists. Britain recently revoked the citizenship of Shamina Begum, who similarly traveled to Syria and wants to return to her country of birth.
Britain asserted that she was entitled for Bangladeshi citizenship due to her heritage, but the Dhaka government on Wednesday denied that she was eligible, leading her to become effectively stateless.
US citizenship is significantly more difficult to lose. The 14th Amendment to the US Constitution, ratified in 1868 after Civil War as slavery was abolished, establishes that anyone born in the country is a citizen with full rights.
In recent years it has been considered virtually impossible to strip Americans of citizenship, even if they hold dual nationality.
The US Supreme Court in the landmark 1967 Afroyim decision rejected the government's attempt to revoke the nationality of a Polish-born naturalized American after he voted in Israel.
And last year a federal judge rejected a government attempt to strip the nationality of a Pakistani-born naturalized American who was convicted in a plot to blow up the Brooklyn Bridge.
But President Donald Trump has campaigned on a hard line over immigration and raised the prospect of ending birthright citizenship ahead of last year's congressional elections.
In 2011, President Barack Obama ordered drone strikes that killed two Americans in Yemen - prominent al-Qaeda preacher Anwar al-Awlaki and his 16-year-old son - but did not believe it was possible to revoke citizenship.
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