The area of Mauthausen has been settled for many millennia, as shown by archaeological discoveries dating back to the Neolithic age.

At the end of the 10th century it became a toll (Maut in German) station for ships, and the name "Muthusen" for the settlement is first mentioned in 1007.

A village that had developed by the Third Crusade was ordered burned on 16 May 1189 by Emperor Frederick Barbarossa when it levied a tax on his army as it marched towards Vienna.

During the Second World War, from 1938 to 1945, one of the first massive concentration camp complexes in Nazi Germany was set up to the west of the town.

Inmates were subjected to barbaric conditions, the most infamous of which was being forced to carry heavy stone blocks up 186 steps from the camp quarry.