Individual items from the Neolithic and Bronze Age have been discovered around Endingen. In the Early Middle Ages the Alamanni settled in the area. The modern village of Endingen is first mentioned in 798 as "Entingas". Until 1945 it was known as "Oberendingen". During the High Middle Ages the major landholders in village included Regensberg, the Bishop of Constance, the Freiherr of Tegerfelden and the lords of Endingen. Starting in the 13th Century the village was under the Habsburgs. After the conquest of the Aargau in 1415 by the Swiss Confederation it was part of the high court of the bailiff of Baden. The low court rights lay with Sankt Blasien Abbey in the Black Forest. The land "herrschaft" rights were held by a number of different owners.