Omaruru was established in 1863 by Wilhelm Zeraua, the first chief of the White Flag clan of the OvaHerero people. In 1871, Anders Ohlsson and Axel Eriksson established a brewery at Omaruru. Eriksson had also established a trading post, which flourished and by 1878 he employed about forty whites. Eriksson's business was based upon long-distance trading between southern Angola and Cape Colony, which necessitated the establishment of regional trade routes.
The town grew around a mission built in 1872 by Gottlieb Viehe, now a museum, and was attacked in 1904 during the Herero Wars. Franke Tower was later erected to commemorate the relief by Hauptmann Victor Franke's troops of the local Schutztruppe garrison, which had been under siege by the Herero people, who had risen against rule by the German colonial empire.