Chief Judicial Magistrate Narender Kumar has directed the 25 accused to appear in Sessions court on June 3, the prosecution said.
One person was killed and several injured as rioters damaged property at Hadoli village under Bhorakala police station in the district on September 8, 2013.
Police had filed charge sheet against 25 people in this case.
The case is related to the communal riots that rocked Muzaffarnagar and neighbouring districts, leaving 60 people dead while thousands of others were displaced.