The University Library was established in 2012 as a foundational pillar to support teaching, learning, and research across all academic disciplines. The initial collection, which totalled approximately 1000 textbooks, was made possible through generous book donations from World Vision, Gulu University, and others. These donations laid the groundwork for what would become a steadily growing academic resource hub.

In 2013, the Library marked a significant milestone by recruiting its first professional librarian, Mr. Bosco Buruga Apparatus, who was tasked with organizing the initial collection, setting up library services for staff and students, and developing library systems and structures.
The implementation of digital library services started in 2014 when the Library became a member of the Consortium of Uganda University Libraries (CUUL). The Library subscribed to eResources through the consortium, which enabled the staff and student to access many eBooks and eJournal articles for their research, academic works, and leisure reading. The Library continued to subscribe to the e-resources offered by CUUL and received others from Research 4 life and Open Access journals and books. It also received, free of charge, the Essential Electronic Agricultural Library (TEEAL) e-resources.

In 2016, the Library installed its first fully featured, open‑source Integrated Library Management System (ILMS) called Koha. The University hired a consultant to develop the system. After installing the ILMS, the library staff were trained and embarked on converting the 4227 catalogue bin cards (print catalogue collection) into the system. The conversion of the print catalogue to digital took about three months from October 2016 to January 2017. In the same year, the Library Website library.muni.ac.ug was developed and launched, and it continues to be informative among university websites in Uganda. In May 2018, the Library installed and customized its Institutional Repository software using Dspace through a consultant hired by the University. The staff were trained on managing and depositing research content as guided by the University Institutional Repository Policy. The repository is growing steadily in terms of collections and items. It has significantly assisted the University in disseminating research conducted by staff and students.

The university council recruited the first substantive University Librarian, the late Dr. Frederick Mukungu, who reported to work on 2nd November 2015. He served the University for five years and retired from service on 30th October 2020. He established new partnerships for the Library. The Library collaborated with Good Steward Global Institute, National Library of Uganda, UNHCR, and Windle International. The Library established libraries in Refugee Camps settlements at Imvepi and Palorinyo in collaboration with the UNHCR (Arua office) and Windle International, with the support of books donated by Good Steward Global Institute from the USA.

Over the years, the Library has grown both in size and capacity. As of 2025, the Library employs nine qualified librarians and houses a rich collection of 10,449 textbooks, serving the diverse academic and research needs of students, lecturers, and researchers. The staffing also improved from one librarian in 2013 to nine in 2025. Two branch libraries have been established: one at the Multi-Purpose Health Science building serving the Faculties of Health Sciences and Science, and another at the Capacity Building Centre (CBC) serving the Faculty of Management Science.
The Library is committed to its vision which is to “be a model library in provision of quality and ICT based information for teaching, learning, and research of Muni University.” As such, the Library continues to evolve, embracing digital resources and modern library management systems to enhance access, efficiency, and academic impact.