Although the Lobatse Musjid only opened its doors in 1967, the history of resident Islam in the country goes back at least a century earlier. During the late 1800s Muslim traders had established a presence in Moshupa, Molepolole, and Ramotswa. For some time thereafter Ramotswa served as the centre of Islamic activity, with the British Indian Mohammadan Society being founded there in 1920, which would ultimately evolve into the Botswana Muslim Association.

While Asian traders of the Muslim faith were active in Lobatse throughout much of the twentieth century, they were barred from settling or establishing shops in the town until after the Second World War. In 1961 they spearheaded the founding of Crescent School.

Before the building of the Musjid in Lobatse, half of the Muslim community used to travel either to Zeerust or Maftkeng in South Africa for Eid festivals. The need to cross the border into the Republic of South Africa was based on the fact that many Muslims in Reproduced by Sabinet Gateway under licence granted by the Publisher (dated 2009). Botswana had relatives in both Maftkeng and Zeerust. Besides, many Muslim children attended school in Zeerust from the mid-1940s to early 1960s.