The present Catholic community in the country finds its roots in the ministry of the Missionary Society of St. Joseph (Mill Hill Missionaries). The origins of the Roman Catholic population of Brunei is traced to the influence of the Spanish missionaries coming mainly from neighbouring Philippines, who also converted the Kadazans in Sabah. Throughout the years, the local Church was administered by various ecclesiastical jurisdictions centred in Labuan, Jesselton (now Kota Kinabalu), Kuching and Miri, cities in neighbouring Malaysia.
The separation of Bruneian territory formerly under the Diocese of Miri-Brunei (now simply known as the Diocese of Miri) created a distinct Bruneian Church. This separated territory was designated as an apostolic prefecture in November 1997, to be headed by then Msgr. Cornelius Sim (who was the Vicar General of Miri-Brunei, and a Bruneian priest) as its first apostolic prefect. On 22 February 1998, the Apostolic Prefecture of Brunei Darussalam came into being with the proclamation of the papal bull to the faithful and the installation of the apostolic prefect. On 20 October 2004, less than seven years after it was formed, the apostolic prefecture was elevated to an apostolic vicariate. However, it remained a suffragan of Archdiocese of Kuching. Msgr. Sim was appointed the first apostolic vicar, carrying the dignity of a titular bishop: his episcopal ordination took place in January 2005.