The Ethnographic Museum at the University of Zurich traces its origins to the collection of the Ethnographic Society of Zurich. The society pursued the goal of building up a collection of objects to enable so-called “ethnological studies”, which at the time was understood as the study of non-European people and their ways of life. The findings were primarily intended as a teaching aid for elementary and middle schools. Prospective merchants who wanted to expand to colonized areas were to be familiarized with non-European cultures. The ultimate aim was thus to expand trading opportunities.

On June 1, 1889, the collection of the Ethnographic Society, in keeping with its economic objectives, opened in the old stock exchange building. It comprised about 500 objects from five private collections. Among them were objects that the zoologist Conrad Keller had acquired at the end of the 19^th century on a trip through East Africa supported by the Federal Council. The collection also included objects owned by the botanist Hans Schinz, who had supported the research trips of the German colonialist Adolf Lüderitz in Southwest Africa and had acquired various objects in the process. 

Missionaries, zoologists, and botanists joined ethnologists in the creation and expansion of the collection in the 19^th century. At the time, ethnology as a scientific discipline was only just emerging and gradually institutionalized.

In 1899, the Ethnographic and Geographic Societies joined forces and formed the Geographic-Ethnographic Society of Zurich (GEGZ). The GEGZ systematically expanded its collection by cultivating a large, closely interwoven network of Swiss planters, engineers, and merchants, who diligently sent objects from the colonies to Zurich.

In the same year, Rudolf Martin was elected director of the collection. At his instigation, an Institute for Physical Anthropology was founded at the University of Zurich. The main focus of the institute was to standardize the measurements of body and skulls, a method known today as "racial research". Rudolf Martin's "Lehrbuch der Anthropologie" became the standard work of so-called "racial anatomy" throughout Europe, and Zurich thus became, in a sense, the center of training for race theorists. Some race researchers who studied in Zurich were later active in the Nazi Reich.

When Rudolf Martin stepped down as director of the GEGZ in 1909, Hans Jakob Wehrli took over as the first trained ethnologist to head the collection. In the years that followed, it grew to such an extent that there was soon a shortage of space. This led to the founding of the Ethnographic Museum in 1913, effectively transferring the collection to the University of Zurich. In 1980, the museum moved to its present location in the Old Botanical Gardens of the University of Zurich. The colonial contexts in which ethnology and the Zurich collection were involved often recede into the background today, despite being the basis for the collection's emergence in the first place.