UNISSA had signed MoU with other universities for cooperation in research, student and staff exchange and other cooperation that benefit both parties. The universities are:
| NO. | INSTITUTIONS |
| 1 | MoU Between The Government of His Majesty The Sultan Yang Di-Pertuan of Brunei Darussalam and The Government of Malaysia on co-Operation in the Field of Higher Education |
| 2 | MoU Universiti Brunei Darussalam (UBD) |
| 3 | MoU The Markfield Institute of Higher Education |
| 4 | MoU International Islamic University Malaysia (IIUM) – DIPERBAHARUI |
| 5 | MoU Al-Azhar University, Arab Republic of Egypt |
| 6 | MoU Cairo University, Egypt |
| 7 | MoU Universiti Teknologi Malaysia, Malaysia (UTM) |
| 8 | MoU Universiti Sains Islam Malaysia (USIM) Malaysia |
| 9 | MoU Institut Studi Islam Darussalam (ISID), Gontor, Indonesia (Tukar : UNIDA) |
| 10 | MoU Universiti Yarmouk, Jordan |
| 11 | MoU Al-Maktoum College of Higher Education, United Kingdom |
| 12 | MoU Universiti Pendidikan Sultan Idris (UPSI), Malaysia |
| 13 | MoU Universiti Malaya (UM), Malaysia |
| 14 | MoU Institut Agama Islam Negeri (IAIN) Sultan Amai Gorontalo, Indonesia |
| 15 | MoU Universitas Islam Negeri (UIN) Syarif Hidayatullah, Jakarta, Indonesia |
| 16 | MoU Universitas Gadjah Mada (UGM), Indonesia |
| 17 | MoU Universiti Sains Malaysia (USM), Malaysia |
| 18 | MoU Universiti Sultan Zainal Abidin (UniSZA), Malaysia |
| 19 | LoI Universiti Kebangsaan Malaysia (UKM), Malaysia |
| 20 | MoU Universiti Putra Malaysia (UPM), Malaysia |
| 21 | MoU Universiti Teknologi Mara (UiTM), Malaysia |
| 22 | MoU Prince of Songkla University (PSU), Thailand |
| 23 | LoI Universiti Malaysia Sabah (UMS), Malaysia |
| 24 | MoU University Fatoni, Pattani Campus Thailand |
| 25 | MoU University of Jordan, Amman |
| 26 | MoU World Islamic Sciences and Education University in Amman, Jordan |
| 27 | MoU Al Al-Byat University, Jordan |
| 28 | MoU Universiti Selangor, Malaysia |
| 29 | MoA Faculty of Law Prince of Songkla University, Thailand with Faculty of Syariah and Law, UNISSA |
| 30 | MoU Islamic Research and Training Institute (IRTI), Jeddah |
| 31 | MoU Daffodil International University, Bangladesh |
| 32 | MoU Islamic University of Malaysia (UIM), Malaysia |
| 33 | MoU Universiti Syarif Kasim, Riau (UIN SUSKA), Indonesia |
| 34 | MoU Kolej Universiti Islam Sultan Azlan Shah (KUIS), Malaysia |
| 35 | MoU Kolej Universiti Islam Perlis (KUIPs), Malaysia |
| 36 | MoU Institut Agama Islam Negeri (IAIN) Sultan Maulana Hasnuddin Banten, Indonesia |
| 37 | MoU Institut Agama Islam (IAIN) Padang Sidimpuan, Sumatra Indonesia |
| 38 | MoU Sekolah Tinggi Agama Islam Negeri (STAIN) Kudus Central Java, Indonesia |
| 39 | MoU University of Darussalam Gontor, Indonesia |
| 40 | MoU International Shari’ah Research Academy for Islamic Banking (ISRA) & FPSP UNISSA |
| 41 | MoU Kolej Universiti Islam Selangor (KUIS), Malaysia |
| 42 | MoU University of Sharjah (UOS), United Arab Emirates |
| 43 | MoU Muhammadiyah University of Metro (MUM), Lampung Indonesia |
| 44 | MoU Universitas Islam Bandung (UNISBA), Indonesia |
| 45 | MoU Kolej Universiti Insaniah (KUIN), Malaysia |
| 46 | MoU Universitas Islam Sultan Agung (UNISSULA) Semarang, Indonesia |
| 47 | MoU Universitas Islam Nadhlatul Ulama (UNISNU) Jepara, Indonesia |
| 48 | MoU Darul Huda Islamic University (DHIU) Kerala, India |
| 49 | MoU Islamic University of Maldives (IUM) Maldives |
| 50 | MoU Egyptian University of Islamic Culture “Nur-Mubarak” Republic of Kazakhstan |
| 51 | MoU Universitas Islam Negeri (UIN) Raden Fatah Palembang Indonesia |
| 52 | MoU Kolej Pengajian Islam Johor (MARSAH) Malaysia |
| 53 | MoU Universiti Kebangsaan Malaysia (UKM) Malaysia |
| 54 | MoU Kolej Universiti Islam Melaka (KUIM) Malaysia |
| 55 | MoU Institut Agama Islam Negeri (IAIN) Bukittinggi, Sumatera Barat Indonesia |
| 56 | LoI Postgraduate Graduate Program Institut Agama Islam Negeri (IAIN) Sumatera Barat Between Centre for Postgraduate Studies UNISSA |
| 57 | MoU International Islamic University Malaysia (IIUM) – DIPERBAHARUI |
| 58 | MoU Universitas Negeri Semarang (UNNES) Indonesia |
| 59 | MoU University of Malaya (UM) Malaysia |
| 60 | MoU Universitas Dharmawangsa Medan (UNDHAR) Indonesia |
| * Memorandum of Understanding (MoU) – 56 * Memorandum of Agreement (MoA) – 1 * Letter of Intent (LoI) – 3 |
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