[3] The parish itself, whose boundaries were much greater than today, reaching as far as the river Senne,[4] seems to predate the 9th century, and from the end of the 12th century, also included a chapel dedicated to Saint Catherine,[5] which, separated from the village by Brussels' city walls, gradually became the current St. Catherine's Church in the Sainte-Catherine/Sint Katelijne neighbourhood of Brussels.

[8][3] This did not prevent the parish priest of Molenbeek from several times being in conflict with the canon of St. Gudula, among other things, about the establishment of a female convent near the St. Catherine Gate in 1238, or about the Beguinage de Notre-Dame de la Vigne (of which the Church of St. John the Baptist at the Béguinage remains today) in 1250, or again about the opening of a school in 1451.

On St. John's Day (24 June), a dancing procession took place, in which epileptics could be freed from their illness for a year if they crossed a bridge over the Molenbeek brook towards the church without their feet touching the ground.

In addition, it was plagued by moisture problems, so by the early 20th century, it was already due for replacement, but the church's Parish Council did not have the resources for such an operation.

The Art Deco building, one of the first churches in Brussels made of reinforced concrete, was built next to the old one, which was demolished once the project was completed, leaving a space where the Parvis Saint Jean-Baptiste/Sint-Jan-Baptistvoorplein was laid out.

The plans were signed on 20 August 1930, the first stone was laid by Cardinal Jozef-Ernest van Roey on 11 May 1931, and the church was inaugurated in 1932.

Above the central portal is a bas-relief by the sculptor Albert Aebly illustrating the baptism of Christ by Saint John the Baptist.

[14] Some interior elements were recovered from the old church, such as the choir stalls, which date from the 17th century, and an 18th-century statue of Saint John the Baptist attributed to Pieter-Jozef Verhaghen.