Wagram was first mentioned in a 1258 tithe register, drawn up when King Ottokar II of Bohemia ruled over the Austrian duchy.

It was named after a now silted up meander of the Danube river, where the waves (German: Wogen) crashed against the shore (Rain).

In 1560 it received the prefix Deutsch- to differ it from Kroatisch-Wagram (today part of Eckartsau), a village founded by Croat settlers in the course of the 1529 Ottoman Siege of Vienna.

[citation needed] In 1580 the population turned Protestant but was forcefully converted in the Counter-Reformation under the Habsburg emperor Ferdinand II shortly afterwards.

[citation needed] Deutsch-Wagram was the location of the 1809 Battle of Wagram fought between invading French troops under Napoleon and an Austrian army led by Archduke Charles.