Yeiner Perez, 24, was arrested in San Francisco and charged with two counts of false imprisonment, four counts of battery and one count of sexual battery, spokesman Alex Bastian said.
He is being held on $100,000 bail, Bastian said.
Perez, who is an acrobat, is scheduled to be arraigned at the San Francisco Hall of Justice Tuesday afternoon.
The charges stem from a May 10 incident at the 16th Street BART station where video showed a fully exposed man doing flips and handstands on fare gates.
He allegedly was harassing people, including kicking and pushing a BART employee and grabbing an elderly customer, injuring her lower back.
He was then taken to San Francisco General Hospital for observation. Upon his release, he was arrested but released a short time later without charges.
Following Perez's release, BART police forwarded the case to the district attorney's office and investigators from that office with the help of immigration officials arrested Perez today and filed charges against him, Bastian said.