In the 16th century the city council accepted the Protestant Reformation officially, and Protestants took over the parish church. The Roman Catholic priest Jan Siński died in the following turmoil. In 1555 King Sigismund II Augustus confirmed religious freedom for the city. In 1616 the St. John's church was restored to the Catholics thanks to local parish priest Jan Doręgowski. In 1620 the first Jesuits came into the town and began the Counter Reformation. In 1622 the Jesuits founded a school, which under the name "Liceum Ogólnokształcące im. Filomatów Chojnickich w Chojnicach" is today one of the oldest high schools in Poland.