Joniškis was established in the beginning of the 16th century. It was mentioned in written sources on 23 February 1536 when Bishops of Vilnius and Samogitia visited the area and found that people still practiced the old pagan faith. People were worshiping the God of Thunder (Perkūnas), fire, snakes and other pagan deities. The bishop of Vilnius, John of the Lithuanian Dukes baptized the locals and established a new parish on 23 February 1536. A wooden church was built and the town of Joniškis was built around it. Bishop of Vilnius named the town Joniškis after his own name Jonas. Joniškis was on the crossroad of important trade roads.