Since its creation in 1499 until the reign of Ferdinand VII, the Universitat de València was governed, directed and economically sustained by the city of Valencia, reason why the Municipal Historical Archive of Valencia holds a great volume of documents generated within the university.

There is little information on the organisation of the university archive throughout the centuries. However, recent studies have enlightened new data on it; for example, the naming of the provost Vicente Martínez de la Raga as provost archivist in 1683, with a salary and a series of duties to carry out as an archivist. Another example is the creation of the Faculty of Medicine Archive in 1712, and the naming of full university professors as archivists, such as Vicente Bartolla and Matías Camarasa, who had to manage the documents that belonged to the medical claustrum and which were kept at the sacristy of the Sapientia chapel.

With the enlightened reforms of the 18th Century, changes are introduced in the Universitat and are reflected in its historical documents. A 1769 Royal Charter orders for a complete index of all papers kept at the University Archive; it was not until 1779 that the Full-University Professors General Senate Board —headed by Joaquín Segarra, canon and principal— began to drawn up this comprehensive index.

The Universitat de València achieved a greater autonomy thanks to the Blasco Plan from 1786; it managed the funds stemming from the city hall. Hence, the archive saw a great rise in the volume of funds and the types of documents.

With the liberal reforms and the fall of the Ancien Régime, the archive started depending on the university's secretary. While the Liberal university was growing and consolidating, the number of documents was also getting higher, enabling a detailed reconstruction of university life from 1845-1857 until today. The universities became part of a more centralised system, with similar tasks for all parts. This fact had an impact on the number of duplicated documents found in the Administration General Archive of Alcalá de Henares.

Since the creation of the Corps of Archivists and Librarians in 1858, the university archives were provided by the staff pertaining to such Corps, who managed antique documents originated from the General Secretary and the University Schools and Faculties. Among them, we can highlight Mariano Rubio y Borrás —sent to the university archive in 1890— or Luis Gonzalvo París, Vicente Ferraz Turmo and Joaquín Casañ Alegre.

During the 20th Century, the university archive was a general character unit of the Bibliographic Information Service. Nowadays, the University Archive is part of the Libraries and Documentation Service and it is composed of the Intermediate Archive and the Historical Archive.