Before the St. Catherine's was built, a 14th-century Dominican church occupied the area.

[2] A monastery was built adjacent to the church, but now the spot is home to the Klovićevi dvori art gallery.

St. Catherine's church was victim to fire twice in history: once in 1645 and again in 1674, devastating the interior.

The church was refurnished with help from wealthy Croatian nobles, and in return, they were allowed to display their family coat-of-arms or have the honour to be buried or entombed in the church.

After the disestablishment of the Jesuits, St. Catherine's became part of the parish of St. Mark's in 1793.