Victor Kamunya alias Doctor Victor and Risper Ogony were accused of unlawfully carrying out a business of pharmacy - on November 3, while not registered as a pharmacists by the pharmacy and poison board.
They were charged with operating the Milan Health International Limited in Kayole jointly with others not before court.
The premises that houses the clinic did not get the approval of the Pharmacy and Poisons board.
They were also charged for operating the clinic and a medical laboratory in a premises not registered with the board.
"Dr" Victor and Ogony were also charged with operating a lab without a license from Kenya Medical Laboratory Technicians and Technologists Board.
The two were arrested after Flying Squad's head of operations, John Njoroge and his team stormed the clinic with Kenya Medical Practitioners and Dentists Board CEO Daniel Yumbya.
"Dr" Victor was found attending to one of the patients at the clinic.
They denied the charges before senior principal magistrate Martha Mutuku
"Dr. Victor studied for clinical medicine at KMTC Siaya campus and completed in July and is due to graduate next month.
Ogony is a first year student of Kiriri Women's University of Science and Technology in Githurai where she is pursuing a Diploma course in procurement.
Her lawyer James Mochere said she had gone to visit someone at the clinic. She was visiting her elder sister who works as a receptionist at the clinic. Mutuku remanded them until Thursday to await a pre-bail report before setting bond terms.
Police are still looking for Mugo after he was named as the owner of the clinic.
Mugo was arrested and charged in 2015 with various offences linked to operating an illegal clinic in Githurai 44, Nairobi and raping a wonam he had allegedly sedated.
He was accused of raping a woman at Prestige Healthcare Clinic on November 1, 2014 after giving her four tablets of an unknown drug.
Prosecution also accused Mugo of operating a pharmacy not registered with the Pharmacy and Poisons Board.
He was also charged with employing two people who are not registered lab technicians and presenting himself as a doctor and purporting to practice medicine without being registered and licenced as a physician.
The "doctor" has denied all the charges and is out on bond as his trial continues.
-Joseph Ndunda