
UIN Sunan Kalijaga has signed Memorandum of Understanding (MoU) with the following organization:
- Arab Academy for Electronic & Information Technology Services, Egypt
- The Institute of Oriental Studies of the Universitat Leipzig, Germany
- Jabatan Kemajuan Islam (JAKIM) Pusat Pentadbiran Kerajaan Persekutuan Putrajaya Malaysia
- The Embassy of Damaskus
- Australian Embassy of Jakarta
- Mennonite Central Committee
- UNESCO, Asian Bioethics Association
- The College of Islamic Studies, Prince of Songkla University, Pattani
- Learning Assistance Program for Islamic Schools (LAPIS) Australia
- Russian Islamic University (Kazan)
- Moscow Islamic University
- The North-Caucasian Islamic Center of Education and Science
- University of Malaya Kuala Lumpur Malaysia
- Georg-August Universitat Gottingen, Germany
- Chemonics International Inc.
- Universiti Teknologi Malaysia
- Tilburg University, The Netherlands
- Academics without Borders Canada (AWBC)
- University of Washington School of Law Legal Education Support Program—Afghanistan (LESPA)
- Embassy of the Islamic Republic of Iran (EIRI)
- Norwegian Centre for Human Rights
- The Southern Border Provinces Administrative Centre (SBPAC) The Kingdom of Thailand
- International Islamic University Malaysia
- Jamiah Zaituna, Tunisia
- International Islamic University, Islamabad Pakistan
- Embassy of Canada
- Indonesian Ambassador for the Republic of Serbia
- International Qur`anic Studies Association (IQSA)
- Universiti Tun Hussein Onn Malaysia
- Civilizations Exchange & Cooperation Foundation (CECF)
- Universiti Teknologi Mara Melaka Malaysia
- University of Sousse Tunisia
- Vrije Universiteit Amsterdam, The Netherlands
- Qatar Charity Indonesia Office
- Special Libraries Association, Asian Chapter (SLA-AC)
- Suez Canal University, Egypt
- Rabitah Jamiat Islamiyah
- University of East London, UK
- Institut Iqra Bintulu Serawak Malaysia
- Amman Arab University, Jordan
- The University of Newcastle, Australia
- Privater Studiengang für das Lehramt für Islamische Religion an Pflichtschulen (IRPA), Austria