The church was built as a part of the row of houses in the place of three burghers´ houses. The municipality of Kežmarok donated them to the Catholic Church in 1650, in order to build up a small church. The present-day Catholic Church of the Holy Cross was namely owned by the Protestants at those times. With this act, the municipality wanted to express their thanks to the prominent persons of the Roman-Catholic Church, who stood on the town´s side in the fights against the castle lords Thököly.

The Holy Cross Church dates back to the times of founding of the Slavonic settlement. Its oldest stone parts (a part of the tower ground floor) come from the Romanesque church from the half of the 13th century. The church as we can see it today comes from 1444 - 1498 when it was greatly rebuilt in the Gothic style. The church has three naves and as it was rebuilt many times it has a unique vault consisting of three types - reticulated, star and cross.