With her face covered by a black dupatta, the 23-year-old was escorted by several police women as she arrived in the court.
The woman, a second year student at a law college here run by Chinmayanand, has accused the former Union Minister of sexually assaulting her repeatedly for a year.
The incident came to light when she went missing on August 24, a day after she uploaded a video on the social media seeking help from Prime Minister Narendra Modi and Chief Minister Yogi Adityanath.
Her family accused the senior BJP leader of kidnapping her.
The woman was tracked down by the state police six days later in Rajasthan.
The Supreme Court took suo moto cognizance of the case and after talking to the girl in the Judges' chamber, the court ordered a Special Investigation Team of the UP police to inquire into her charges.
The woman claims she went into hiding after gathering video proof to substantiate her allegations against Chinmayanand, a powerful politician who was Minister of State for Home in the Atal Bihari Vajpayee-led BJP government.
Chinmayanand, who runs several ashrams and institutions, allegedly helped her with her admission into the law college and urged her to move into the hostel.
The BJP leader is accused of calling her to his room, blackmailing her with a clip of her taking a bath and raping her repeatedly. The woman also alleges she was often taken to his room by his aides at gunpoint and forced to give him massages.
The video clips of Chinmayanand being given a massage have already gone viral on the social media.
( With inputs from IANS )