The Jesuit community that was already settled in Vitoria in the 18th century has existed for 16 years. The college was founded in 1751 and it was dedicated to San Fernando in honor to the monarch that conceded them the permit to found the building in the capital. Before that, the Jesuits were settled in private homes but they were not permitted to build a community until the middle of the 18th century. The Society of Jesus had tried to create a community in Vitoria two times at the end of the 16th century and another one at the end of the 17th century. The authorities and great part of the clergy did not permit that the Jesuits settled in the city by alleging that Vitoria already counted on several religious communities. The last time that they tried to found a Jesuit school was in 1737, when the general Juan Francisco de Manrique y Arana left a legacy to found a Jesuit church and school, which were finally carried out in Villa Suso. The founding took place when Ferdinand VI and Benedict XVI approved it by a Royal Decree issued on the 18th of April 1751 and a Papal Bull issued on the 29th of April. The pope gathered in a letter all the reticences stated without reasonable cause by the secular and regular clergy. On the 19th of May, when Calahorra's bishop was in Vitoria, he sent the document through which the "Casa de habitación" was built in the city. It belonged to the two Jesuit Fathers that lived in it, either the school or the house of residence of the Society of Jesus, according to the regulations approved by the Apostolic See... There is little information about the buildings that were constructed; the church was Baroque style, the most characteristic style of the Society of Jesus. It is not known if the school was inaugurated and used as a school because at the end of 1766, the communities from Vitoria (canonries and the rest of religious communities) decided to expel the Jesuits from the city and to cancel the community's founding. It was abolished by the Royal Decree issued on the 27th of February and the Pragmatic Sanction issued on the 2nd of April 1767, ordered by Charles III. In the following two years, all these immovable properties that belonged to the College of San Fernando in Vitoria were sold. The church was demystified and destroyed because it was considered not to be necessary for the worship. The school turned to its previous functions as a home for laypersons.

At the end of the 19th century, a group of Jesuits with French origins tried to return to Vitoria; in 1942, the Society founded the “colegio-instituto politécnico Jesús Obrero”.