But with the Islamic State group down to its last stretch of land, Muthana said she has renounced extremism and wants to return home with her toddler son, born to one of her three jihadist husbands.
But Muthana's lawyer says that she is a USA citizen and holds a US passport.
Mr Trump said on Twitter he has "instructed" Secretary of State Mike Pompeo "not to allow Hoda Muthana back into the country" - a break with usual U.S. protocol not to comment on individuals' immigration issues.
Muthana now has an 18-month-old son from one of her ISIS marriages.
On Feb. 20, ISIS looked close to defeat in its last enclave in eastern Syria on Wednesday as civilians poured out, and the USA -backed Syrian Democratic Forces (SDF) said the remaining jihadists wanted to fight to the death, Reuters noted. Begum's lawyer has said the family is considering all legal avenues to challenge the decision.
The refusal to admit 24-year-old Hoda Muthana could set precedent and face legal challenges as it is generally extremely hard to lose USA citizenship.
Now, Muthana begs to be let back into the U.S.
A lawyer for the woman's family, Hassan Shibly, said the administration's position is based on a "complicated" interpretation of the law involving her father.
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".
An attorney representing Muthana's parents claims she is a US citizen despite the fact that her father was serving as a Yemeni diplomat when she was born in New Jersey, which, according to the State Department, means she is not entitled to birthright citizenship. "The Trump administration continues its attempts to wrongfully strip citizens of their citizenship".
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According to U.S. Citizenship and Immigration Services, a child born in the United States to an accredited foreign diplomat is not subject to U.S. jurisdiction and therefore is not eligible for citizenship under the 14th Amendment.
Under the Immigration and Nationality Act, a person born in the U.S.to a foreign diplomatic officer is not subject to US law and is not automatically considered a USA citizen at birth.
US President Donald Trump said on Twitter that he had "instructed" Pompeo to prevent Muthana's return.
Hoda Muthana wrote that she made "a big mistake" by rejecting her family and friends in the United States to join the Islamic State. Both of her terrorist husbands were reportedly killed in war.
In a separate tweet responding to Trump, Shibly said the United States is "a nation of laws and we must hold everyone accountable to them".
A huge debate has sparked in the United Kingdom over the future of Shamima Begum, a British teenager who hopes to return back to the United Kingdom in order to raise her newly born child.
Meanwhile, other countries are facing similar decisions about what to do with Muslims who joined the Islamic State in Iraq and Syria. During her time in Raqqa, Syria she has been married three times, given birth to a son and been active on the now-deleted Umm Jihad Twitter handle.
Shibly said Muthana was brainwashed online before she left Alabama and now could have valuable intelligence for USA forces.
Begum is living in a Syrian refugee camp, where she gave birth to a boy last weekend.
Secretary of State Mike Pompeo refused to allow an Alabama-born "ISIS wife" to return to the United States Wednesday; blocking her request despite her public apology for joining the Islamic State in Syria. "I regret it. I hope America doesn't think I'm a threat to them and I hope they can accept me and I'm just a normal human being who's been manipulated once and hopefully never again".