The name of the church comes from the chapel of St. Catherine founded in 1360 by the Municipal Council of The New City of Torun. According to the legend, nuns living here initiated the baking of gingerbreads called Catherine's (katarzynki). This word may be associated with the great annual fairs held on St. Catherine's day during which the products of Torun gingerbread makers were especially popular.

The present church was constructed in the neo-Gothic style at the end of the 19th century.