Sub-inspector Nurunnabi of Bhujpur Police Station filed the case on Thursday night against 100 named and 4,900 unnamed people.
Thirty-four people, including Bhujpur UP chairman and Jamaat leader Shafiul Alam Nuri, who were arrested on Thursday in connection with the clash, were shown arrested in the case, police said.
Meanwhile, she Section 144 imposed in the area following the clash still remained in force.
Besides, police and members of Rapid Action Battalion and Border Guard Bangladesh were kept deployed in the area to fend off any untoward incident.
Three people were killed and about 120 others, including cops, injured in the clash involving activists of Awami League and Jamaat-Shibir-Hefajat and villagers at Kazirhat in upazila on Thursday afternoon.
Over 100 motorcycles, four mini trucks, three private cars, a fire service vehicle and a microbus were also torched during the clash.