Chief U.S. District Judge Michael Davis ordered Amina Farah Ali, who cited religious reasons for not rising, to be taken into custody by federal marshals on the first day of the trial for her and a co-defendant, Minnesota Public Radio reported.
Ali, dressed in a black hijab, was handcuffed and escorted out of the courtroom by a marshal.
About 45 minutes later, the Rochester woman was called back into the courtroom and asked if she would stand, as ordered.
"I'll not stand for anyone except for Allah," Ali replied.
Davis said she could remain in the courtroom for jury selection but would be required to watch the trial from a monitor in another room.
"No one is asking her to give up her religion," Davis said. "She does not have a First Amendment right not to stand."
The judge said her behavior is "disruptive and causes great harm to the administration of justice."
Her lawyer will be allowed to take breaks to consult with her, MPR said.
Ali, 35, and co-defendant Hawo Mohamed Hassan, 64, also of Rochester, have both said in pretrial motions they're not guilty and that they raised money for humanitarian causes in Somalia, which has been beset by coups, civil war, drought and famine, the St. Paul Pioneer Press reported.
Prosecutors allege Ali and Hassan raised money in the Somali-American community for al-Shabaab, which the United States considers a terrorist organization.
Court filings indicate the government alleges evidence will show the two women transferred money to terrorists, and that Ali helped coordinate and pay for the travels of seven men who wanted to fight with al-Shabaab in Somalia.