Mugo wa Wairimu pleaded not guilty and has previously denied that he raped his patients after sedating them.
The charges stem from a Kenyan TV report which had footage showing an unidentified man allegedly assaulting an unconscious woman on a clinic bed.
Kenya's Medical Practitioners Board has said he is not a registered doctor.
Mr Wa Wairimu went on the run for a week after the report was aired on Kenya's private Citizen TV.
He was eventually arrested at a hotel outside the capital, Nairobi, after members of the public called the police.
The secretly recorded footage was filmed by a suspicious staff member.
The BBC's Odhiambo Joseph in Nairobi says Mr Wa Wairimu has been in custody since his arrest, as it was argued that releasing him might endanger his life because of the public outrage over the affair.
The court ordered on Friday that he remain in custody until Monday 5 October when his bail application is to be heard.
In one of the last posts on his Facebook page before his arrest, he described the allegations against him as "malicious".
"Mob justice, media or otherwise only replaces due process in failed states. Kenya is not Iraq, Syria or Yugoslavia," wrote Mr Wa Wairimu, who is also a blogger.
He was able to do a few Facebook posts on Friday around the time of the court hearing, reiterating that he was "unbowed" and said "may justice be our shield and defender".
A Kenyan man has been charged with 12 offences including rape, impersonating a gynaecologist and operating a clinic without a licence in Nairobi.