Palazzo Badoer derives from the “house of the priory of San Giovanni Evangelista” belonging to the Badoer family. A document from 1350 granted the Badoer family the right to bury the members of the Confraternity of San Giovanni Evangelista: the cemetery still exists beneath the palace hall, and its presence historically shaped the unusual floor plan of the building (which can be outlined in the shape of a “Z”), distinguishing it from the typical Venetian palace layout.
Subsequent works, leading to the formally completed architectural configuration that survives today, are documented up to 1712; further interior works were carried out in later years.

In 1974 Iuav purchased the palace from the Institute of Santa Caterina, the Sisters of Nevers.
Extraordinary maintenance and functional adaptation works for its use as the Department of Architectural History began in April 1978.

Since 2008 Palazzo Badoer has been the home of the Iuav Doctoral School.