Gupta, who was working as secretary at Sahkari Samiti Prasiddhpur, is accused of supplying arms, ration, vehicles and money to Ram Vriksh Yadav.
Gupta was arrested from near Ataina bridge under Usaihat police station area on the Badaun-Farrukhabad border, District Magistrate Chandra Prakash Tripathi said.
He has been taken to the police lines where senior officials are questioning him, the DM said.
Earlier on Wednesday, another accused in the Mathura incident Chandan Bose and his wife Suman were arrested in Basti by a team of Mathura police.