Alison Ernst, 36, entered the pleas to misdemeanor counts of trespassing and violence against a person during her arraignment late Wednesday in U.S. District Court in Las Vegas.
U.S. Magistrate Judge Cam Ferenbach then granted the government's request to keep Ernst in federal custody, saying she was a flight risk and danger to the community. She is being held at a jail operated by a federal contractor in Pahrump, 63 miles west of Las Vegas.
Ferenbach raised concerns about Ernst's residency status and mental health condition, Natalie Collins, a spokeswoman for the U.S. Attorney's office in Nevada, told The Associated Press.
The judge appointed a federal public defender to represent her and set a June 25 trial date before U.S. Magistrate Peggy Leen.
Ernst's public defender, William Carrico, did not immediately respond to requests for comment Friday.
Ferenbach also directed the U.S. Probation Office to prepare a report detailing Ernst's criminal history, if any.
Federal authorities have not disclosed a motive in the case yet.
According to the criminal complaint, Clinton was speaking at an April 10 conference at the Mandalay Bay resort when Ernst walked up to the stage area and threw a soccer shoe at Clinton. The shoe passed near Clinton's head, causing her to flinch and duck, but it did not strike her. Clinton cracked a couple of jokes before resuming her talk.
Ernst wasn't a credentialed conference attendee and should not have been in the ballroom, authorities said. She somehow got past people checking tickets at the entrance, they said, and she was arrested immediately after the shoe was tossed.
Clinton, the former secretary of state, first lady and Democratic senator from New York, has been traveling the country giving paid speeches to industry organizations and Democratic Party groups. She has said she's seriously considering a presidential bid.
If Ernst is convicted of both federal charges, she could face up to two years in federal prison and the possibility that federal authorities would be able to monitor her movements under terms of supervised release.