The FIR was registered late evening at Versova police station on the complaint of the woman who alleged that Pandey harassed her by posing to her obscene questions and passing lewd remarks inside a hotel room in Mathura on March 4 during the BJYM's three-day executive committee meeting.
In her written complaint to BJP city unit president Ashish Shelar, the woman had stated that Pandey also "held her hand" when she tried to leave the room.
Police said Pandey was booked under appropriate section of IPC on the woman's complaint.
The BJYM leader had denied the allegation against him by terming it as a fallout of a "political conspiracy" and internal bickering in the BJYM.
After the woman gave the written complaint to Shelar on March 22, he dissolved the Mumbai unit of BJYM.
The issue was raised in state Legislative Council by women legislators yesterday, following which Chief Minister Devendra Fadnavis announced a probe by the State Women's Commission.