Universitas Gadjah Mada Archives was officiated on 11 September 2004 by Rector of UGM, Prof. Dr. Sofian Effendi, and Head of Indonesian National Archives(ANRI), Drs. Djoko Utomo, MA. Previously, the management of UGM archives, particularly inactive archives, were run by a separate unit, Records Center, that was operationally under the Administrative and Household division.

After the change of UGM status into State-owned Legal Entity University, based on Board of Trustee Decree dated 18 October 2003 on UGM Articles of Association, it was stated that Universitas Gadjah Mada Archives, along with, PPTiK, KP4, LPPT, PPP, and Academic Hospital, were established as university supporting facilities.

Initiation of University Archives establishment was started after an agreement extension between ANRI and UGM with the signing of a Memorandum of Understanding on 3 October 2002 by Prof. Dr. Sofian Effendi (then Rector of UGM) and Dr. Mukhlis Paeni (then Head of ANRI), which was a milestone for Universitas Gadjah Mada Archives. Intensive meetings between ANRI officials and the Rector produced an agreement to realise the MoU. Technical matters were managed by Faculty of Cultural Sciences. The Faculty later appointed Archiving Diploma Programme to prepare the establishment of the University Archives. Facilitated by ANRI, the Archiving Diploma Programme for two years (end of 2002 to mid- 2004) conducted research and feasibility study to prepare for the establishment.

On 11 September 2004, Universitas Gadjah Mada Archives was officiated by Rector of UGM, Prof. Dr. Sofian Effendi, and Head of ANRI, Drs. Djoko Utomo, M.A. After the inauguration, the University Archives was situated on the Pantja Dharma hall in the Sekip area. Since July 2012, the University Archives moved to the Universitas Gadjah Mada Library and Archives compound in Bulaksumur area on the third floor of L7 building.