Before the year of 1780 there was a post mill on the site of this mill. That mill had been blown over and repaired, but in the year 1780 it was demolished and replaced by the present hexagonal mill. The Molen van Waardenburg is one of the eight remaining hexagonal mills in the Netherlands.

For many years the mill belonged to the Waardenburg-Neerijnen estate. In the First World War, the windmill was used to generate electricity. After the high water levels in the river Waal in 1995, the dike of the river was made heavier and raised, after which the mill was also raised by one and a half meters.

Because of its location, the corn mill is considered being one of the more beautiful mills in the Netherlands. Since 2009 the mill is owned by Stichting Geldersch Landschap & Kasteelen, a foundation for the protection of nature and landscape in the province of Gelderland. The mill is still regularly used for grinding grain by volunteers.