Grootfontein was originally known as Otjivanda to the Herero people. It forms part of the Otavi Triangle, highly fertile area with high rainfall and a flourishing agricultural sector.

During the year 1885, 40 Boer families who were part of the Doersland trekkers settled in Grootfontein on their way to Angola. Their trip was cut short when the Portuguese took over the country. These families turned back and formed the Republic of Upingtonia back in Grootfontein.

Hwoever, in the year 1887 it became abandoned and in the year 1893 Grootfontein became the headquarters of the South African West Company. 

In 1896 a German Schutztruppe Fortress was built but eventually abandoned. In the present day, this fortress is being used as a museum dedicated to the local history of the town. 

For many years Grootfontein made their profits by being part of the mining industry.  The Berg Aukas and Abenab mines were located to the north east of the town. For decades, zinc and vanadium were mined but it did not last long.

However, Grootfontein is a dolomite area and carbonate deposits found in the upper parts of the mines have shown fossils of simian or pongoid creatures.