Human settlement in the San Fernando de Henares area dates back to the Neolithic, and proof of this are the local archaeological sites. But San Fernando de Henares was truly born in 1756, when King Felipe V ordered the creation of a royal tapestry factory. In a place close to the cities of Madrid and Alcalá de Henares, called Torrejón de la Ribera, a factory of extra-fine cloths was set up so that production would not depend on foreign imports.
Houses were built in front of the factory, initially thought for the factory workers, leading to the origin of the current town. The layout and construction of the new town followed the urban planning notions of the European Baroque period of the first half of the 18th century.
In 1753, the factory moved to Vicálvaro due to its low productivity, with the warehouses remaining in San Fernando.
During the French occupation, the Real Sitio de San Fernando de Henares was strongly damaged.
In 1829, the factory building, that had been used as hospice, was transferred for a royally protected factory of cotton and printed fabrics to be established there.
Between 1842 and 1846, the gardens were renewed, with 4,000 fruit trees being planted, and the streets and walkways were organised. In 1860 a railway was built in San Fernando. In 1864, the Real Sitio is sold to private purchasers whose main activity is farming and cattle breeding.
In 1868, the township stopped belonging to the monarchy and being the Real Sitio de San Fernando de Henares, and established its own town hall.
In 1916, the village changed its name from San Fernando de Jarama to its current name San Fernando de Henares. Between 1920 and 1922 electricity reached the village and in 1931 the first telephone line arrived.
In the 1960’s the village was industrialised, and the primary sector practically disappeared. Many people migrated to San Fernando, mainly from Castile La Mancha, Andalusia and Extremadura. New houses and infrastructures were built.
In 1968, the Planning and Coordination Commission of the Madrid Metropolitan Area approved the first Urban Development General Plan for San Fernando, in the framework of joint development with Coslada. This will set up the new residential quarters that will mainly define great part of the current San Fernando.
In 1983, the historical centre is declared historic-artistic site.