The Musjid was completed around 1882, though some sources suggest as early as 1861, by members of the South Australian Afghan community. These “Afghans” were generally Muslims from then-British India, with some coming from Afghanistan and the Middle East. They worked as camel drivers and breeders in the region. It is estimated that about 3,000 “Ghans” were involved in this work until cars and trains became prevalent in the 1930s.

The Musjid was constructed by camel breeder Abdul Kadir, owner of Wangamanna Station. Another cameleer, Mullah Assim Khan, became imam of the Marree Musjid in the early 20th century. The town had two Musjids for a time, but the northern one was abandoned around 1910. Another report suggests a Musjid was deliberately demolished in 1956 by its elderly caretaker, Syed Goolamdeen, who could no longer maintain it.

As of 2003, it was reported that the descendants of the Afghans in Marree had rebuilt the Musjid. However, a heritage survey conducted from April 2001 to June 2002, funded by the Australian and South Australian governments, reveals that the Musjid no longer exists apart from an area of prepared ground and post stubs, and the nearby remains of an enclosure for camels. The heritage survey, published in 2002, reports that a “replica Musjid” had been built within the Marree township. A tourist map published in 2018 shows a Musjid within a park called the “Afghan Cameleer Park,” located within the alignment of the former Central Australia Railway which passed through the town.