History of St. Stephen’s Church dates back to the very beginning of Kouřim’s history. The exact time of its foundation is still unknown. Remains of reused Romanesque blocks were found in the masonry of the building, which most probably came from the building of the older church. It existed even before the foundation of the medieval town, the oldest written record of which dates back to 1261.

After 1270, the main and south naves were fully completed, and it was probably not until the turn of the 13th and 14th centuries that the top floors of both towers were erected. Medieval history of St. Stephen’s Church is not sufficiently known due to the lack of extant written sources. The oldest surviving record of it dates back to 1334, when the building was damaged by a fire that engulfed the entire town. At the beginning of the 15th century the interior was decorated with valuable wall paintings. ,