The name Jouy-le-Moutier has only been in use since the 13th century. Two charters by Charlemagne to the bishop of Paris, Eschenradus gave the chapter of Notre Dame de Paris the possession of the church of Andrésy. When the parish of Jouy was created the chapter of Andrésy became its owner. There is no known nomination at the parish of Jouy before 1186.
In 1250 the parish of Vauréal was created from part of the parish of Jouy. Once again it was the chapter of Notre Dame de Paris who chose the first vicar of Jouy. Two letters dated of the 2 April 1250 from Renaud de Corbeil, bishop of Paris, authorised the parish of Jouy-le-Moutier to build a baptismal church.
The monks of Saint Martin-des-Champs owned in Jouy land and a hostel. The Cistercians of Notre-de-Dame-du-Val (near L'Isle-Adam) were also owners of land as early as the 13th century. The rich Benedictine of the abbey of Saint Martin-des-Champs built in the 12th near the Fontaine à Jouy a building called La Maison des Moines which was used as a cellar. Wine growers paid their taxes in wine. The main agriculture of Jouy was wine as well as fruit growing.
At the beginning of the 20th century the village saw the arrival of the railway. A viaduct crossing the Rue de la Vallée was built in 1912 carrying the CGB line from Maurecourt to Pontoise following the River Oise valley.
In 1978 the village saw the construction of a thousand new dwellings on the plateau in relation to the creation of the new town of Cergy-Pontoise. The population grew from 1,200 to 10,000 in less than 5 years. Today most administrative duties are still performed in the village's town hall.