The establishment of Universitas Wiraraja cannot be separated from the role and dedication of public figures, educators, entrepreneurs, and the Government in Sumenep Regency. This campus, located at the eastern tip of Madura Island, East Java, was founded with the pioneering efforts of Drs. H. A. Said Hidayat, M.Si, Head of the Department of Education and Culture of Sumenep Regency (1985-1995); Soegondo, Regent of Sumenep (1985-1995); Waseol Djakfar, BBA., Head of the Sumenep Learning Activity Center; and Syafrawi, an employee of Bank Negara Indonesia 1946. On Friday, July 25, 1986, corresponding to the 18th of Dzulqa'dah 1406 Hijri, the Yayasan Universitas Wiraraja Sumenep was established as a legal entity organizing Universitas Wiraraja, founded with the notarial deed by Abdul Kohar, SH., a Notary in Surabaya, Number: 159. This foundation later established a private university named Universitas Wiraraja. Subsequently, the governing body underwent a transition from the Yayasan Universitas Wiraraja to the Yayasan Arya Wiraraja based on the Decree of the Minister of Research, Technology, and Higher Education Number: 473/KPT/I/2016.

Initially, Universitas Wiraraja offered four programs: the Department of Agricultural Social Economics, the Department of Law (Specialization in Civil Law), the Department of Business Management, and the Department of Public Administration.

In line with community needs, Universitas Wiraraja expanded its offerings by adding programs such as Civil Engineering, Accounting, Nursing, Diploma III Midwifery, Professional Nurse Program, Natural Science Education, PGSD, Master's in Law, and Agricultural Product Technology, most of which are accredited with B, and the Law program is accredited with A.

Since 2018, the Public Administration program has changed its nomenclature to Public Administration Studies. In 2019, Universitas Wiraraja opened new programs including the Bachelor's Midwifery and Professional Midwife Program. Between 2020 and 2022, several new programs were introduced, such as Bachelor's Programs in Informatics, Information Systems, Digital Business, and Visual Communication Design. Universitas Wiraraja was also accredited with the rating "EXCELLENT" by the National Accreditation Board for Higher Education (BAN-PT) in 2020.

Universitas Wiraraja continuously develops its facilities, including adding lecture halls and four new classrooms, expanding the library, language laboratory, computer laboratory, civil engineering laboratory, micro-teaching laboratory, integrated science laboratory, mock trial court, Wiraraja Medica Clinic, greenhouses, tax center, mini bank, BI corner, business incubator, Indonesian Syariah Stock Exchange Investment Gallery, Maharaja Center, FISIP laboratory, THP laboratory, Informatics laboratory, Graha Sumekar, Graha Wiraraja I, and computer-based test (CBT) center.

Furthermore, Universitas Wiraraja now provides and develops data and information services that can be widely used by academic staff and the community, along with improving the quality of human resources for faculty and educational staff through training and advanced studies to provide quality service for students. The university also offers insurance programs for all students as a form of health and nursing guarantee. In 2022, Universitas Wiraraja established the Restorative Justice House, making it the first university in Indonesia to have such a program.

Universitas Wiraraja supports and facilitates the development of student creativity by encouraging participation in various student activities and continually fostering good coordination, communication, and cooperation with local governments, companies, regional educational institutions, the Ministry of Education and Culture, as well as regional and international organizations. This is done to enhance the implementation of the Merdeka Belajar � Kampus Merdeka program and improve the quality of education that will produce professional, globally competitive graduates with a national character to face the era of Society 5.0.