The clerk's office for the Missoula District Court says Johnson appeared in court Tuesday morning.
Prosecutors allege Johnson raped an acquaintance in February after she invited him to her room to watch a movie. He has been charged with sexual intercourse without consent.
Attorney Dave Paoli has said Johnson "strongly maintains his innocence."
Johnson's attorney is asking a judge to dismiss that charge and for prosecutors to turn over text messages between students and university administrators involved in the investigation.
Johnson declined to comment as he left to be fingerprinted and booked into jail.
Johnson had been slated as the Grizzlies' starting quarterback. He was suspended after being charged July 31.