The Library of Atma Jaya Catholic University of Indonesia was established in 1960 and was initially located within the Santa Ursula High School complex. Its initial collection was donated by The United States Book Exchange, which was collected by R. Marsidi and Ben Mang Reng Say. The first head librarian was Nancy Lo Siang Hien Ginting, who was assisted by Evelyn Hilman. The library moved to the Semanggi Campus in 1971. Over time, the library developed itself in several specialized fields.

• The Center for Society Development Studies (PKPM) Library, established in 1972, has collected more than 60,000 titles of books, research reports, journals, magazines, as well as other publications in the form of videos, microfilms, and CDs. The library is also equipped with a unique collection of archives and history about Indonesia before the independence era. Complete publications from various international organizations, such as the World Bank, WHO, UNCTAD, SALUS, and the Center for the Study of New Religious Movements in Primal Societies, are also stored here.
• The Center for Language and Culture Studies (PKBB) Library, which began its construction on February 1, 1980, specializes in the fields of theoretical and applied linguistics and language teaching, particularly the latest publications and journals. The up-to-date and diverse collection, consisting of over 9,000 book titles and 84 magazines or journals from domestic and international sources, makes the PKBB Library a reference point for faculty members and students in the linguistics and language teaching graduate programs from various universities in Indonesia. The PKBB Library played a significant role in facilitating the opening of the Postgraduate School's Applied English Linguistics Program (LTBI) in October 1992.
• Perpustakaan Fakultas Kedokteran Unika Atma Jaya memiliki lokasi khusus pada tahun 1990, bersamaan dengan kepindahan operasional Fakultas Kedokteran ke Kampus Pluit. Hal ini supaya mahasiswa dan dosen Fakultas Kedokteran sangat dimudahkan dan dapat dilayani dengan koleksi yang lebih berfokus pada bidang ilmu kedokteran dan kesehatan. The Library of Medical Faculty of Atma Jaya Catholic University of Indonesia had its dedicated location in 1990, coinciding with the relocation of the Medical Faculty's operations to the Pluit Campus. This was done to provide convenience for medical students and faculty members and to focus the collection on medical sciences and health-related fields.

In 2001-2002, as a final project of several students from the Faculty of Engineering, the first version of the library catalog and information system was developed, equipped with a Graphical User Interface (GUI) to make it more user-friendly (previously, it only had a text-based interface). However, at that time, the catalog could only be accessed from within the campus.

Since 2006, the library has been organizing structured user education activities for new students every year. This activity, known as IT4U, has been held as part of the Campus Introduction program coordinated under Path III since 2011. In that year, AtmaLib underwent a transition to the new AtmaLib, which was developed alongside the academic system. In this new system, back-end and front-end activities were conducted through a single portal accessible from both inside and outside the campus.

In 2009, the library became one of the first units to enter the scope of ISO 9001:2008 quality management system certification at Atma Jaya Catholic University of Indonesia, along with the Faculty of Engineering, Faculty of Biotechnology, and the Office of the Rector.

In 2010, the library expanded its space, including four rooms on the ground floor of Building G, which were used for multimedia services, discussion services, computer services, and a collection of old books.

Furthermore, in 2014, the library underwent a complete spatial renovation, consolidating the operations of the PKPM Library, previously located on the second floor of Building K2, and the PKBB Library, previously located on the fourth floor of Building K2, into the Central Library on the third floor of Building E.

In 2017, the library established a new service point at the BSD Campus, with the main function being similar to the Central Library, providing library materials for the three pillars of academic activities conducted at the campus.