Pompeo issued a statement earlier in the day saying Muthana is no longer a U.S. citizen and will not be allowed back into the country.
"She does not have any legal basis, no valid U.S. passport, no right to a passport, nor any visa to travel to the United States. We continue to strongly advise all U.S. citizens not to travel to Syria," he said.
Muthana, 24, left Alabama in 2014 to join the militant group and marry an IS fighter. She told Britain's The Guardian newspaper she made a "big mistake" and that she was brainwashed into the decision.
She's seeking to return to her U.S. home along with her 18-month-old son. Muthana is living at the al-Hawl refugee camp in northern Syria.
"I look back now and I think I was very arrogant. Now I'm worried about my son's future. In the end I didn't have many friends left, because the more I talked about the oppression of ISIS the more I lost friends. I was brainwashed once and my friends are still brainwashed," she said, using an acronym for the militant group.
Muthana's lawyer, Hassan Shibly, said the woman's birth certificate shows she was born in Hackensack, N.J., in 1994.