The University of Navarra Library Service was created as a set of departmental libraries in parallel with the formation of the first Schools. The Main Library was established in 1961 and combined the collections of the Schools of Humanities and Social Sciences, Law, and Canon Law. The other two sections that make up the current Library Service, the Geographical and Social Sciences and the Experimental Sciences, were created later.

Today, the Humanities and Geographical and Social Sciences sections are combined into a single section and housed in the Main Library Building. The Experimental Sciences section occupies a building located near the Schools of Medicine, Pharmacy and Sciences. There is also a third library in the School of Architecture.

In 1983, the Library Service began the process of computerizing its collections using DOBIS-LIBIS, thus making it one of the first Spanish libraries to implement automated systems. In 2000, this system was replaced by INNOPAC MILLENNIUM.