Reuben Kiborek is accused of committing the criminal act at a five star hotel within Nakuru County on the eve of Christmas.
Kiborek who was before Senior Resident Magistrate Yvonne Khatambi was charged with two counts of defilement and alternative indecent act.
The accused however denied all charges after spending three nights in police custody.
He arrived in court at 11.30am accompanied by his lawyer and was sneaked into the courtroom through the back-door, perhaps in a bid to escape hawk-eyed journalists who came to cover the case.
Kiborek's friends who had turned up in court, shielded the accused from journalist cameras as they whisked him out of the court precincts. In court Kiborek covered his face when charges were read to him.
He was arrested on December 23 and detained at Bondeni Police Station awaiting to be arraigned in court.
The sexual assault of the 16-year-old girl is alleged to have happened at one of the town’s five-star hotels on Sunday night.
The suspect is alleged to have picked up the minor from their home on Sunday afternoon and drove her to the Hotel where he committed the act. The girl then reported the matter to her parents who in turn informed the police.
Kiborek is reported to have fled the hotel immediately after the act and the police mounted a man-hunt for him by various police teams, including the special crimes unit.
The suspect was later tracked down and arrested by police officers who drove him back to Nakuru for him to face the charges.
The suspect was first booked at Bondeni Police Station where he was interrogated by detectives from the Directorate of Criminal Investigations.
And immediately the accused was directed to the dock, Kathambi ordered that "all journalists and anybody who is not Kiborek relatives" out of court.
The hundreds of his friends, mostly men who were allowed to enter the courtroom, whisked the accused out of the precincts after he was arraigned.
Case is set to be mentioned on January 18, 2019 for the setting of a hearing date.