A small number of Jews lived in Wageningen during the 1560s. They were allotted ground for a cemetery and one of their numbers was permitted to lend money against property taken as security. The Jews were expelled from Wageningen sometime during 1570 or 1571.

In 1668, a Jew was granted permission to lease the local municipal lending bank. In the same year, a Jewish cemetery was established on the Stadsbleek, the present-day Kerkhofpad, near the Veerstraat. The cemetery was also used by Jews from elsewhere in the surroundings to bury their dead. The lease for the cemetery grounds was permanently assigned to the Wageningen Jewish community in 1760; the cemetery was expanded a year later. At the time, the Jews of Wageningen worked in the tobacco and meat trades as well as operating the local lending bank.

The Jewish community at Wageningen was officially granted independent status in 1830; prior to then, local Jews had officially belonged to the community at Arnhem. In the early years of the community, Wageningen Jews prayed in a private home. A synagogue was furnished in a building on the Riemsdijkstraat in 1839. In 1903, this synagogue was replaced with a new one in a building on the Walstraat. In 1913, the Wageningen community opened a new cemetery located on the Oude Diedenweg. The old cemetery on the Kerkhofpad was closed in 1929.

The Jewish community at Wageningen was governed by a board. Voluntary organizations included a burial society and a women's society that cared for the interior of the synagogue.

Wageningen was home to the Landbouwhogeschool Wageningen, Netherlands' leading institution for the study of agriculture, the present-day Wageningen University. During the 1920s and 30s, a relatively large number of Jews studied at the school, many in preparation for emigration to Palestine.

In 1940, the first year of the World War II German occupation of the Netherlands, the Jewish population of Wageningen increased due to the arrival of foreign Jews expelled from the coastal districts of the country. 1940 also saw the expulsion of Jewish instructors from the agricultural school at Wageningen as part of countrywide anti-Jewish measures. A number of students at the agricultural school staged a strike in protest. The majority of the Jews of Wageningen were deported and murdered during the war. A few dozen, however, managed to survive the war in hiding. The synagogue was struck by a bomb in May of 1940, during the first days of the war. The building and its contents went up in flames.

A small number of Jews returned to Wageningen after the war and managed to maintain a community until 1987 when the Jewish community at Wageningen was officially dissolved and the locale was placed under the aegis of the Jewish community at Arnhem.

The Jewish cemetery on the Kerkhofpad was declared a national monument in 1967 and was restored 20 years later. A monument in memory of the murdered Jews of Wageningen was unveiled on the Walstraat in May of 2000. The names of the 72 Jews from Wageningen and nearby Rhenen, Renkum, and Ede murdered during the Second World War are also memorialized in the regional museum De Casteelse Poort.

The Jewish population of Wageningen and surroundings:

The size of the Jewish community over time