In early medieval times the region was partially property of the powerful monasteries of Ilmmünster and Münchsmünster, and partially divided into tiny secular states. One of those states was the county of Scheyern. The counts were ancestors of the Wittelsbach family, who in 1180 became rulers of Bavaria. From that time on the region was a part of Bavaria.
The district of Pfaffenhofen was established in 1972 by merging several former districts.