Inspector General, Aligarh Range, Sanjeev Gupta, informed about the arrest in Kasganj to media persons.
The main accused Salim is said to be a cloth merchant and had fired a bullet from the terrace of a building that fatally hit Gupta. Accomplices Nasim and Wasim are said to be absconding.
On January 26, Gupta, 22, had died when two groups of different communities exchanged fire over a Tiranga Yatra in Kasganj.
At least three shops, two buses and a car were torched after Gupta was killed in clashes following stone-pelting by a mob on a motorcycle rally taken out to celebrate the Republic Day.
Candle marches had also been taken out in Chandan's memory in Allahabad and Aligarh on Monday.
As many as 118 people were arrested in connection with the violence.
UP CM Yogi Adityanath said the culprits of the violence would not be spared. The Centre has sought a report from the state government.
Firebrand BJP leader and Union Minister Giriraj Singh said that he felt the violence was pre-planned.
"Had the deceased been Mohammad Ismail instead of Chandan Gupta, there would be been a different debate in the media...We have to change this mindset," Giriraj Singh told reporters.