The foundations of the Baptist movement that now exists in the Czech Republic began in the mid-19th century. At that time, mission work took place primarily among the German-speaking inhabitants. The first independent Baptist church was founded in 1885 in Hleďsebi u Veltrus.', 'The movement expanded, and in 1919 an association of Baptist churches were established and named the Brethren Union of Chelčícky.

The original union consisted of 25 churches.  The name later changed to the Brethren Baptist Union (of Chelčický). In the Union’s fiftieth year the name was simplified to the Brethren Baptist Union.  All of the Czech Baptist churches were within the Czechoslovakia area until the end of 1993.  On January 1, 1994, Czechoslovakia separated into the Czech Republic and Slovakia.  The Brethren Baptist Union divided into two independent organizations—the Czech Baptist Union and the Slovak Baptist Union. They have worked to stay in close cooperation with each other.  They do many activities together, inform each other, use the same hymnal with Czech and Slovak songs, and produce the Rozsievač magazine and so on.