Many immigrants in Glengary Township and the surrounding area were Catholics of Czech and Irish descent. During the early years few priests were available, so they visited the community whenever possible beginning in 1874. Local parishioners conducted prayer services regularly when priests were not present. The chapel, the first permanent house of worship in Fillmore County, was built in the 1870s on the Josef Kotas form northwest of this cemetery. A successor church, St. Wenceslaus Catholic Church, was erected in the newly formed town of Milligan in 1890.
Burials commenced here before Anton Svec purchased the property from the Burlington & Missouri River Railroad in 1878. He deeded two acres for a cemetery to his Czech brethren in 1887. Although known locally in earlier years as the Catholic Cemetery, and later as the North Cemetery, it was incorporated as the Cesky Bratri (Czech Brethren) Cemetery Association in 1904. The chapel was moved to the cemetery from the Kotas farm in 1901. The building was restored and dedicated as the Pioneer Chapel in 1998.