The church was built outside the town walls, on land owned by the Prague Chapter, outside the range of the Sedlec Monastery, and was dedicated to St. Barbara, the miners' patron saint. Founded in 1388, most of the construction was financed by the miners themselves. The impressive structure which, according to some historic sources, had been planned at twice its current length, was erected in stages, and depended to a large extent on the prosperity of the local mines. All sorts of events interrupted the construction several times and more than 500 years elapsed between the start and the definitive completion of the project in 1905.
Kutná Hora had always wanted to be a match for Prague and it was certainly not by mere coincidence that Prague builders and architects had been sent for to take part in the construction. Johann Parléř, son of Peter Parléř, the builder of St. Vitus's Cathedral in Prague, was the first designer of St. Barbara's. Hence the correspondences between the Kutná Hora church and the cathedral in Prague. As silver mining gradually declined, the financial resources slowly dried out, and a provisional wall terminating the church was built in 1558.
In 1626, the church was handed over to the Jesuits and was largely Barocised. The unique structure then remained unfinished for over 300 years. In 1884, the town authorities, inspired by the local archeological society, Vocel, decided that construction should be resumed. The project was definitively completed in 1905. The architecture of St. Barbara's is a textbook example of the development of Gothic architecture in Bohemia.