The Museum library is made up of approximately 2000 volumes, largely dedicated to the history of science. There is a small historical collection with ancient volumes which are displayed in the museum rooms on rotation.

The library provides an on-site consultation and document delivery service to users who request it. The catalog can be consulted online via the University Opac.

The Museum archive, with documents that refer to a long chronological period (from the beginning of the 15th to the 20th century), has a composite nature, with materials of various origins. Part of the documents were transferred to the Museum at its foundation (in the 1930s) from the University archives or from other University institutes that were being closed or transferred to other locations; another part were purchased from antiquity dealers and privates, or came through donations. In some cases, however, it is not possible to accurately reconstruct the process of acquisition of the documents.

For the most part, the documents relate to medical studies, though some concern the history of the University as a whole and all its disciplines, both scientific and humanistic. Overall, the Archive is an important integration of what is preserved in the State Archives of Pavia (the ancient University archive) and in the Historical Archives of the University.

The inventory of the material can be consulted on site and, in part, online on Lombardia Beni Culturali.