Trump's refusal to admit 24-year-old Hoda Muthana comes just as he is pressing Europeans to repatriate their own Islamic State fighters and will likely face legal challenges, with USA citizenship extremely hard to lose.
Currently, Muthana and her son are living at a refugee camp in northern Syria.
In a brief statement on Wednesday, the U.S. secretary of state said Hoda Muthana, 24, "is not a USA citizen and will not be admitted into the United States". So she duped her parents into thinking she was going on a college trip, and instead bought a plane ticket to Turkey with her tuition money.
President Donald Trump suggested on Twitter on Wednesday that he directed Pompeo to bar Muthana from re-entering the U.S.
Earlier this week, the British government revoked the citizenship of United Kingdom citizen Shamima Begum, who left the country at the age of 15 to join IS in Syria.
Muthana's father was a Yemeni diplomat, and children born in the United States to active diplomats are not bestowed birthright citizenship, since diplomats are under the jurisdiction of their home countries.
"I would say that the situation of American citizens or possible American citizens in Syria is by definition extremely complicated, and we're looking into these cases to better understand the details", said State Department spokesman Robert Palladino in a press briefing on February 19.
In this file photo taken on February 22, 2015, Renu Begum, eldest sister of British Islamic State member Shamima Begum, holds a picture of her sister while being interviewed by the media in central London.
But a United States official said a later investigation showed that she had not been entitled to her passport, adding: "Ms. Muthana's citizenship has not been revoked because she was never a citizen".
The announcement by Pompeo comes just two weeks after the U.S. State Department issued a statement calling on its allies to repatriate their own citizens detained in the conflict. The New York Post reported that she could face up to 60 years in federal prison for her support of ISIS.
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According to Mia Bloom, who tracks female jihadis at Georgia State University, "She was one advocating for extreme violence, especially against American military and servicemen".
In her latest interview, Muthana told ABC: "I'm a normal human being who has been manipulated".
Muthana, who dodged sniper fire and roadside bombs to escape, is ready to pay the penalty for her actions but wants freedom and safety for the son she had with one of two Isis fighters she Wednesday, he said.
She was married three times and has a toddler son.
Secretary of State Mike Pompeo said in a statement released on Wednesday that Muthana's request will not be accommodated.
She is joined there by another woman, Kimberly Gwen Polman, 46, who had studied legal administration in Canada before joining the caliphate and who possesses dual United States and Canadian citizenship. Muthana's lawyer says the administration's position is based on a "complicated" interpretation of immigration law. If she applies for a passport and is rejected, she's entitled to challenge that.
Her Twitter feed was "full of bloodcurdling incitement", according to The Guardian.
Hassan Shibly, a family representative for Muthana, denied that she was not a citizen, and called the move by the Trump administration to claim otherwise "very risky".
"I was really young and ignorant and I was 19 when I made a decision to leave".
"I thought I was doing things correctly for the sake of God", she said, adding that she was "brainwashed once and my friends are still brainwashed".