Alison Ernst had entered the pleas late Wednesday in Las Vegas federal court to counts of violence against a person and trespassing.
US Magistrate Judge Cam Ferenbach found that the 36-year-old Ernst was a flight risk and danger to the community and ordered her to remain in federal custody.
He appointed two federal public defenders to represent her and set a June 25 trial date.
Ernst is charged with bypassing security to enter the Mandalay Bay resort ballroom where Clinton was speaking on April 10. The shoe missed Clinton, and Ernst immediately surrendered to authorities.