It is not known when the first church was built in Hoensbroek. A chapel was built sometime between the 11th and the 14th centuries. In 1390 the chapel was elevated to church status, although as an annex of the St. Pancratius church of Heerlen. Possibly the tower, nave and choir were all built shortly thereafter, largely of marl and in a simple late-Romanesque style. The tower originally could only be entered from the inside of the church.

IThe church was probably built right away as a three-aisled basilica. The nave was covered by a flat wooden ceiling and a clerestorey with small windows, much like those on the church of Noorbeek, provided daylight. When in 1516 the interior was rebuilt in Gothic style, with new pillars, arches and vaults transforming the church into a pseudo-basilica, the clerestorey lost its purpose. The side-aisles were raised, providing space for larger pointed windows, and all three aisles were covered by a single roof. In 1680 the choir was heightened and lengthened, mostly with bricks. The windows in the side-aisles were altered in Baroque style. In 1725 a brick sacristy was built at the south side of the church.

Throughout its history the church remained in catholic hands, as the village was part of the Spanish, later Austrian Netherlands from 1661 until 1795. By the end of the 19th century the church was in a bad state and had become much too small, and there were serious plans to replace it by a new church. Thankfully, permission to demolish the old church was denied, and the new church eventually was built on the other side of the road. The parish now owned two churches within short distance from each other, both called St. Jan. To distinguish the two, the old church was usually called Kleine St. Jan ('little St. Jan)  while the new one was nicknamed Grote St. Jan ('big St. Jan). The old church was restored  in 1909-1910 by architect W. Sprenger. The side-aisles were given separate lectern roofs again, thus once more revealing the clerestorey.  

Despite the restoration, the church was not used for several more decades, and due to neglect and mine damage fell into decay once more. In 1954 another restoration was finally carried out. It has since been used as a secondary church.