The origin of this church is to be found in China (Kwantung Province), an area of the Hakka. In 1847 missionaries of the Basel Mission had started evangelistic work among the Hakkas in Hong Kong and, more generally, in South China. For political and economic reasons many Hakkas emigrated to North Borneo, which had come under indirect British rule in 1878. The first Christian group reached Kudat in 1882; others were to follow and to settle at different places in North Borneo. They set up a loose association of “Basel congregations.” In 1907, at the request of the colonial regime, the Basel Mission established direct relations with them, intending to establish an independent church in North Borneo. The realization of the project was prevented by World War I. In 1925 the church became independent. After the formation of Malaysia (1963), the church adopted its present name.
In 1974 the church began evangelistic work among the indigenous people of the area (Bumiputra). The number of indigenous believers quickly increased, and today Malay-speaking Christians outnumber Chinese-speaking members. The new congregations plan to form their own synod by the year 2000.
The BCCM is the leading member of an association of different Sabah churches, which run the Theological Seminary of Sabah (Seminari Theologi Sabah) in Kota Kinabatu.
Though the structure of the BCCM is genuinely Ref (autonomy of congregations, elected lay president, strong lay participation in decision-making bodies, periodical election of headpastor, who is called bishop), the church is a full member of the LWF. This is because the Basel Mission combined Luth and Ref traditions from the very beginning; it also chose to have close relations with the Tsung Tsin Mission in Hong Kong (TTM).