Tracy McIntosh asked to change his December 2004 plea and instead go to trial.
Common Pleas Judge Pamela Pryor Dembe, however, denied his request.
The charges stem from McIntosh's encounter with a 23-year-old woman who was applying to graduate school at Penn.
The two went out to dinner in 2002 so he could show her around campus. Prosecutors allege that McIntosh drugged the woman with an animal sedative from his lab and raped her in his office.
McIntosh is the former director of Penn's Head Injury Research Center. The university forced him to resign.
