The municipality has 16 divisions: Neuburg has been inhabited since the Bronze Age with artifacts discovered on the hill where the modern palace is located.

[3] A Roman settlement was also located on the high hill overlooking the Danube, providing a part of the Limes, the border between the Empire and its Germanic enemies.

During the Thirty Years' War, the city was conquered and occupied several times between 1632 and 1634 during the battles for Regensburg by Swedish troops passing through here, while crossing the Danube.

On 30 June 1972, Neuburg an der Donau became a Grosse Kreisstadt (similar to a county seat) and was passed to Upper Bavaria region.

Grünau is a renaissance hunting lodge of Elector Otto Henry, which is situated 7 km further east (built from 1530 onwards).