He was later produced in the court which remanded him to 14-day judicial custody. Earlier, Chinmayanand was taken to the district hospital for medical examination following his arrest.
The arrest comes on the complaint of a 23-year-old law student who had accused Chinmayanand of blackmail and rape by posting a video message on the social media on August 23.
The very next day, the woman went missing and was later found in Dausa, Rajasthan.
Taking suo moto cognisance of the incident, the Supreme Court called the victim for a closed door hearing and later ordered the Uttar Pradesh government to set up a Special Investigating Team to probe the allegations. The court also ordered security for the victim and her family.
Chinmayanand, meanwhile, had been evading questioning by the SIT. Earlier this week, he complained of 'uneasiness' and 'weakness' and was kept under house arrest in his ashram.
He was treated by a team of doctors at his ashram and was later shifted to the hospital after his condition showed no signs of improvement.
On Thursday night, doctors advised him to shift to Lucknow for treatment, but Chinmayanand refused.
However, questions were being raised on the working of the SIT. The victim had recorded her statement under Section 164 of the CrPC, but the SIT failed to arrest or question the BJP leader. Rather he was kept under house arrest at his ashram.
Apparently dismayed at the delaying tactics, two days ago the victim threatened to commit suicide if Chinmayanand was not arrested.
The woman, who studied in a college run by Chinmayanand, said in her statement that the self-proclaimed godman got a video of her made while she was taking bath in the college hostel and used it to blackmail her. She claimed that she was raped several times by Chinmayanand, who threatened to eliminate her family if she raised her voice.
The matter also turned into a major controversy after the Supreme Court intervention, and the opposition accusing the Yogi Adityanath government of favouring Chinmayanand and avoiding his arrest.
( With inputs from IANS )