Mohamad Jamal Khweis, a 26-year-old facing charges of providing material support to IS, was ordered held without bail at the hearing in his home state of Virginia.
The case could shed new light on a trend that has seen IS successfully recruit disenchanted youths, including from Europe and the United States, to fight on its behalf.
Khweis voluntarily gave himself up to Kurdish peshmerga forces on March 14 near Sinjar Mountain in Kurdish-controlled territory in northern Iraq, according to an affidavit submitted by a special agent with the Federal Bureau of Investigation.
Sporting a timid look and not saying a word, Khweis looked over to his relatives seated in the courtroom, just hours after the unsealing of a federal criminal complaint against him.
"It was good to see him," Khweis's father said.
Khweis returned to the United States from the northern Iraqi city of Erbil late Wednesday, when he was placed in US custody.
Defense attorney John Zwerling suggested he may seek to throw out the government's evidence, which is based on statements his client gave to Kurdish and FBI officials.
"Everything is not as it appears in the government's pleadings," Zwerling told reporters.
Asked whether Khweis had been treated well while detained by Kurdish authorities, Zwerling simply responded "now he is," after being taken into US custody.
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Khweis is due back in federal court in Alexandria, just outside Washington, on Tuesday for a detention hearing and on June 21 for a preliminary hearing.
- 'Gave himself' to IS -
Through a search of his electronic devices, investigators found that Khweis had been researching IS since December, with images of the World Trade Center burning on September 11, 2001, IS fighters and leaders, as well as maps of Iraq, Syria and Turkey, including known IS bastions.
During an interview with federal investigators, Khweis "stated he 'gave himself' to ISIL and that they controlled him," the affidavit read, using an acronym for the IS group.
"The defendant stated he was aware that ISIL wants to attack and destroy the United States. The defendant stated that ISIL wants America to be taken over."
In a video released online days after his arrest, Khweis describes his contacts with IS before stating that he had renounced the group's violent, extremist ideology.
Khweis later told the FBI that he had "provided misleading information in the video for self-protection," according to the affidavit.
During his interviews, Khweis said he was initially inspired to join IS because he believed they were engaged in "peaceful and humanitarian efforts."
In Turkey, on his way to IS territory, he used the code phrase "green bird" indicating his support for violent jihad, or holy war, in order to make IS recruiters feel at ease in dealing with him.
While staying in an IS safe house in Raqa, Syria, Khweis said he told another IS member he wanted to become a suicide bomber, though stressing he had believed the question was intended as a test of his commitment to IS, according to the affidavit.