Originally, a small church used to stand on the site and has been dated as early as 1238. Bishop Jan IV. of Dražice started a large reconstruction at the beginning of 14th century, which completely wiped out the original character of the church. Archbishop Arnošt of Pardubice carried on with the reconstruction and his successor Archbishop Jan Očko of Vlašim consecrated the finished church on 4th May 1371. Right from the beginning the church was a parish church and from 1625, with the exception of the communist era, was a monastery church of the neighbouring Dominican convent.

The church of St. Jiljí on Husova Street in Prague’s Old Town has in its west facia a couple of unevenly tall steeples. The taller one has a tall pyramidal roof with a lantern is 58.5m high, the smaller steeple is 43.5 m high. Both steeples used to be of the same height, the same as the south steeple. The north one lost its height several centuries ago on 28th June 1432. On that date during a strong hail storm, lightning struck the church and set fire to the north steeple. The frame with its slated roof burned out and the blaze melted the suspended bells. The same lightning killed a woman in front of the main altar, who was praying for her drowned husband, an Old Town fisherman.

The damage done to the property was repaired immediately but the north steeple was only given a temporary low roof. This provisional arrangement however has lasted until today and not only was the steeple not restored to its original height but it was also left with the temporary elliptical roof.