"I thought I was doing things correctly for the sake of God", Muthana told the Guardian.
An attorney for the woman's family, Hassan Shibly, said the administration's position is based on a "complicated" interpretation of the law involving her father.
Trump's comment came hours after Mike Pompeo insisted that Muthana did not have United States citizenship.
Muthana said her curiosity about religion soon became a major part of her life, and watching scholars lecture about Islam on YouTube led her to memorizing portions of the Koran.
It also comes as the USA urged allies to take back citizens who joined IS, but are now in the custody of the American-backed forces fighting the remnants of the brutal extremist group that once controlled a vast area spanning parts of Syria and Iraq.
She said they were brainwashed and interpreted what they were told by predatory ISIS members 'very wrong'.
Muthana's father was a Yemeni diplomat to the USA, according to reports, and the children of diplomats are not typically granted birthright citizenship since diplomats are considered under the jurisdiction of their own country. President Trump made it clear that she wasn't coming back.
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.
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.
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Muthana used social media accounts to connect with extremists in the Middle East before traveling there and once there used them to spread calls to action among ISIS supporters.
Hoda Muthana left Alabama to join IS when she was 19, and this week pleaded with authorities to let her come home.
Her father, Mohammed, told BuzzFeed he gave his daughter a smartphone after she graduated from Hoover High School in May 2013.
In fact she was smuggled into Syria, where she met up with the Islamic State and began urging attacks in the West. "She is not entitled to US citizenship", he said.
Muthana escaped Islamic State territory in January and is now in a refugee camp in Syria with her son, according to reports. After he was killed, she married another, the father of her son. "This is the right place for me to live and I am really ready to die, to meet my God as a true Muslim". Now, she says she "deeply regrets" supporting the terrorists and inciting hatred on social media.
Muthana grew up in Hoover, Alabama, and left the U.S. traveling to Syria to join ISIS in 2014. Go on drivebys, and spill all of their blood, or rent a big truck and drive all over them. "I turned to my religion and went in too hard".
Her lawyer argues that she was born in the USA, specifically New Jersey in 1994; her citizenship status prior to leaving to join ISIS remains unclear.
She added that she hopes Americans will "excuse me because of how young and ignorant I was".
Iraqi Shiite fighters from the Popular Mobilization units take off an Islamic State flag from an electricity pole on March 3, 2016, during an operation in the desert of Samarra aimed at retaking areas from ISIS jihadists.