The construction of the chapel was likely part of an effort of Kutná Hora’s burghers and miners to become independent of the Sedlec Monastery that controlled ecclesiastic administration in the Kutná Hora region. On the rocky headland above the Vrchlice River construction of the karner – a two-story cemetery chapel with an ossuary - began in the mid 1380's.
The chapel's lower area is among the few entirely preserved areas from the high Gothic period: it is vaulted by nine cross-ribbed vaults to four massive cylinder-shaped pillars. It is illuminated by three windows from the east and was originally entered from the west and south through built-in staircase ramps.
Bones were walled in during the 1640´s. Walling in bones was one of the Jesuits' first steps in preparing for further usage of the chapel. It became the oratory and place of exercises of pious brotherhoods. The chapel was not used after the order was abolished (1773) and was sold to the Snížek family in 1797. The chapel changed owners throughout the 19th.century. It was purchased in 1886 by Jan Tuček who set up an organ workshop here. The factory disappeared after WWII.
It was on the list of the world's 100 most endangered landmarks in the 1990s. Thanks to the effort of the town of Kutná Hora and the Ministry of Culture, CZK 20 million worth of reconstruction was carried out from 1997 to 2000 to save the chapel.