There are following well known Indonesian Universities:
- University of Darussalam Ambon
- University of Pattimura
- University of Udayana
- University of Bale Bandung
- University of Balikpapan
- University of Syiah Kuala
- University of Muhammadiyah Aceh
- University of Serambi Mekkah
- University of Lampung
- University of Bandar Lampung
- University of Muhammadiyah Lampung
- Institute e Teknologi Bandung
- University of Pendidikan Indonesia
- University of Komputer Indonesia
- University of Katolik Parahyangan
- University of Kristen Maranatha
- University of Islam Bandung
- University of Pasundan
- Institute e Teknologi Nasional
- University of Widyatama
- University of Islam Nusantara
- University of Advent Indonesia
- University of Langlangbuana
- University of Nurtanio
- University of Nasional Pasim
- University of Informatika Dan Bisnis Indonesia
- University of Sangga Buana
- University of Padjadjaran
- University of Trunojoyo
- University of Islam Kalimantan M A B Banjarmasin
- University of Lambung Mangkurat
- University of Agustus Banyuwangi
- University of Putera Batam
- University of Internasional Batam
- University of Batam
- University of Riau Kepulauan
- University of Baturaja
- University of Dayanu Ikhsanuddin
- University of Islam
- University of Presiden
- University of Bengkulu
- University of Muhammadiyah Bengkulu
- University of Dehasen Bengkulu
- University of Al Muslim
- Institute Pertanian Bogor
- University of Ibn Khaldun
- University of Pakuan
- University of Nusa Bangsa
- University of Djuanda
- University of Galuh Ciamis
- University of Suryakancana
- University of Jenderal Achmad Yani
- University of Muhammadiyah Cirebon
- Institute Seni Indonesia Denpasar
- University of Mahasaraswati Denpasar
- University of Pendidikan Nasional
- University of Warmadewa
- University of Hindu Indonesia
- University of Dwijendra
- University of Ngurah Rai
- University of Gunadarma
- University of Indonesia
- University of Flores
- University of Garut
- University of Negeri Gorontalo
- University of Muhammadiyah Gresik
- University of Mercu Buana
- University of Katolik Indonesia Atma Jaya
- University of Tarumanagara
- University of Trisakti
- University of Paramadina
- University of Al Azhar Indonesia
- University of Darma Persada
- University of Negeri Jakarta
- University of Pancasila
- University of Kristen Krida Wacana
- University of YARSI
- University of Persada Indonesia YAI
- University of Muhammadiyah Jakarta
- University of Jayabaya
- University of Pembangunan Nasional Veteran Jakarta
- University of Nasional
- University of Budi Luhur
- University of Bunda Mulia
- University of Respati Indonesia
- University of Bhayangkara Jakarta Raya
- University of Islam Jakarta
- University of Multimedia Nusantara
- University of Indraprasta PGRI
- University of Sahid
- University of Krisnadwipayana
- University of Prof Dr Moestopo
- University of Tama Jagakarsa
- University of Satya Negara Indonesia
- University of Islam As-syafiiyah
- University of Satyagama
- University of Mpu Tantular
- University of Timbul Nusantara
- University of Agustus
- University of Islam Attahiriyah
- University of Bung Karno
- University of Ibnu Chaldun
- University of Azzahra
- University of Suryadarma
- University of Bina Nusantara
- University of Esa Unggul
- University of Kristen Indonesia
- University of Muhammadiyah Prof. Dr. Hamka
- University of Jambi
- University of Batanghari
- University of Sains Dan Teknologi Jayapura
- University of Cenderawasih
- University of Yapis Papua
- University of Jember
- University of Muhammadiyah Jember
- University of Islam Jember
- University of Pesantren Tinggi Darul 'ulum
- University of Darul 'ulum
- University of Nusantara PGRI Kediri
- University of Islam Kadiri
- University of Haluoleo
- University of Muhammadiyah Kendari
- University of Widya Dharma
- University of Muria Kudus
- University of Kuningan
- University of Nusa Cendana
- University of Katolik Widya Mandira
- University of Muhammadiyah Kupang
- University of Islam Darul Ulum
- University of Islam Lamongan
- University of Samudra Langsa
- University of Malikussaleh
- University of Muhammadiyah Luwuk
- University of Katolik Widya Mandala Madiun
- University of Merdeka Madiun
- University of Muhammadiyah Magelang
- University of Tidar Magelang
- University of Majalengka
- University of Kristen Indonesia Toraja
- University of Hasanuddin
- University of Atma Jaya Makassar
- University of Muhammadiyah Makassar
- University of Makassar
- University of Negeri Makassar
- University of Muslim Indonesia
- University of Brawijaya
- University of Negeri Malang
- University of Merdeka Malang
- University of Ma Chung
- University of Widya Gama
- University of Kanjuruhan Malang
- University of Islam Malang
- University of Gajayana
- University of Wisnuwardhana
- University of Katolik Widya Karya
- University of Tribhuwana Tungga Dewi
- University of Muhammadiyah Malang
- University of Sam Ratulangi
- University of Klabat
- University of Nusantara Manado
- University of Katolik De La Salle
- University of Negeri Papua
- University of Mataram
- University of Muhammadiyah Mataram
- University of Sumatera Utara
- University of Negeri Medan
- University of Muhammadiyah Sumatera Utara
- University of Islam Sumatera Utara
- University of Methodist Indonesia
- University of HKBP Nommensen
- University of Darma Agung
- University of Muslim Nusantara Al-wasliyah
- University of Pembinaan Masyarakat Indonesia
- University of Medan Area
- University of Prima Indonesia
- University of Pembangunan Panca Budi
- University of Setia Budi Mandiri
- University of Alwashliyah
- University of Dharmawangsa
- University of Dian Nusantara
- University of Tjut Nyak Dien
- University of Amir Hamzah
- University of Musamus Merauke
- University of Muhammadiyah Metro
- University of Islam Majapahit
- University of Mayjen Sungkono
- University of Andalas
- University of Bung Hatta
- University of Putra Indonesia Yptk Padang
- University of Muhammadiyah Sumatera Barat
- University of Tamansiswa
- University of Ekasakti
- University of Negeri Padang
- University of Baiturrahmah
- University of Palangka Raya
- University of Bina Darma
- University of Muhammadiyah Palembang
- University of Indo Global Mandiri
- University of PGRI Palembang
- University of IBA
- University of Kader Bangsa
- University of Sriwijaya
- University of Cokroaminoto Palopo
- University of Tadulako
- University of Islam Madura
- University of Madura
- University of Bangka Belitung
- University of Yudharta Pasuruan
- University of Pekalongan
- University of Riau
- University of Islam Riau
- University of Muhammadiyah Riau
- University of Simalungun
- University of Muhammadiyah Ponorogo
- University of Tanjungpura
- University of Panca Bhakti
- University of Muhammadiyah Pontianak
- University of Purwakarta
- University of Jenderal Soedirman
- University of Muhammadiyah Purwokerto
- University of Wijaya Kusuma Purwokerto
- University of Muhammadiyah Purworejo
- University of Kristen Satya Wacana
- University of Mulawarman
- University of Agustus Samarinda
- University of Darwan Ali
- University of Dian Nuswantoro
- University of Islam Sultan Agung
- University of Katolik Soegijapranata
- University of Stikubank
- University of Semarang
- University of Muhammadiyah Semarang
- University of Agustus Semarang
- University of AKI
- University of Wahid Hasyim
- University of Diponegoro
- University of Negeri Semarang
- University of Sultan Ageng Tirtayasa
- University of Serang Raya
- University of Muhammadiyah Sidoarjo
- University of Sunan Giri
- University of Jabal Ghafur
- University of Pendidikan Ganesha
- University of Panji Sakti Singaraja
- University of Abdurachman Saleh
- University of Pamulang
- University of Subang
- University of Veteran Bangun Nusantara
- Institute Teknologi Sepuluh Nopember
- University of Airlangga
- University of Kristen Petra
- University of Negeri Surabaya
- University of Narotama
- University of Katolik Widya Mandala Surabaya
- University of Dr. Soetomo
- University of Ciputra Surabaya
- University of Pembangunan Nasional Veteran Jawa Timur
- University of Agustus Surabaya
- University of Widya Kartika
- University of Hang Tuah
- University of Bhayangkara Surabaya
- University of PGRI Adi Buana
- University of Wijaya Kusuma Surabaya
- University of Muhammadiyah Surabaya
- University of Pelita Harapan Surabaya
- University of Surabaya
- University of Wijaya Putra
- University of Katolik Darma Cendika
- University of Yos Soedarso
- University of Tri Tunggal
- University of Surabaya
- University of Sebelas Maret
- University of Muhammadiyah Surakarta
- Institute Seni Indonesia Surakarta
- University of Slamet Riyadi
- University of Surakarta
- University of Setia Budi Surakarta
- University of Kristen Surakarta
- University of Sahid Surakarta
- University of Tunas Pembangunan
- University of Nahdlatul Ulama
- University of Islam Negeri Syarif Hidayatullah Jakarta
- University of Swiss German
- University of Islam Syekh-Yusuf
- University of Pelita Harapan
- University of Maritim Raja Ali Haji
- University of Borneo
- University of Siliwangi
- University of Pancasakti
- University of Islam Indragiri
- University of Kutai Kartanegara
- University of Kristen Tentena
- University of Khairun
- University of Muhammadiyah Maluku Utara
- University of Halmahera
- University of Negeri Manado
- University of PGRI Ronggolawe
- University of Sains Alqur'an
- University of Gadjah Mada
- University of Islam Indonesia
- University of Muhammadiyah Yogyakarta
- University of Negeri Yogyakarta
- University of Islam Negeri Sunan Kalijaga Yogyakarta
- University of Kristen Duta Wacana
- University of Atma Jaya Yogyakarta
- University of Sanata Dharma
- University of Pembangunan Nasional Veteran Yogyakarta
- Institute Seni Indonesia Yogyakarta
- University of Teknologi Yogyakarta
- University of PGRI Yogyakarta
- University of Mercu Buana Yogyakarta
- University of Respati Yogyakarta
- University of Sarjanawiyata Tamansiswa
- University of Janabadra
- University of Cokroaminoto Yogyakarta
- University of Proklamasi '
- University of Widya Mataram
- University of Ahmad Dahlan
