In 1991, the Islamic Academy of Education, a not-for-profit trust committed to the upliftment of minorities, was established by the entrepreneur Mr. Yenepoya Abdulla Kunhi as its Chairman. The trustees perceived a hiatus in the area of Health Professional Education and so decided to start a Dental college. Within a very short span of time, the Yenepoya Dental College (1992) was granted permission by the Dental Council of India to educate aspiring students to become dentists. Soon, with one successful milestone after another, the Trust launched the Yenepoya Institute of Nursing Sciences (1994), the Yenepoya Medical College (1999), the Yenepoya Nursing College (2002), and the Yenepoya Physiotherapy College (2003). All these colleges offer Graduate and Postgraduate programmes. From its inception, the management dreamt of providing quality education, and towards this goal hired highly qualified teachers, who have since proved themselves to be the best in their profession. In a healthy campus, with natural surroundings, the trust raised buildings designed to bring out the best learning, in the distant suburbs of Mangalore.
The Islamic Academy of Education in its quest towards excellence in professional education, decided to sponsor the formation of a new trust with the sole purpose of creating a Deemed-to-be- University in 2007. Recognizing the yeoman service provided over the years by these institutions, the Ministry of Human Resource Development, Union of India, on the recommendation of the University Grants Commission granted recognition to Yenepoya University Trust a Deemed-to-be- University status under Section 3A of the UGC Act,1956 in 2008. This opened a new chapter in the history of Yenepoya Institutions.