Mekane Yesus Seminary, as a training institute of the Ethiopian Evangelical Church Mekane Yesus, was established in 1960. Mekane Yesus Management and Leadership College (MY-MLC) was started in 1995 as a department of the Seminary. At first MY-MLC offered two-year diploma level courses in Management, Leadership, Development and Communication. In 2005 the College upgraded its education to Bachelor level in order to serve better both the Ethiopian Evangelical Church Mekane Yesus (EECMY) and the communities of the country at large with full accreditation of HERQA. The College is working to produce trained personnel through provision of quality education in Leadership and Development, Gender and Development, and Accounting and Finance, and Management. The main objective of the College is to help all of its students and staff to aspire for high ethical standards and to develop their knowledge and skills for the benefit of the Ethiopian and African societies through maintaining excellence in learning and teaching.

The highest decision-making body in the EECMY is the General Assembly which meets every four years. The issue of developing training capacities of the Church training institutions, especially MY-MLC, was brought to the attention of the 16th General Assembly. The General Assembly thoroughly discussed the matter and resolved that MY-MLC shall grow to Mekane Yesus University by adding more disciplines and upgrading its training gradually to Master and Doctorate levels. Based on the resolution of the General Assembly, the Council of the Church, which is the second highest decision-making body of the Church, decided in July 2013 to start Master's level training at MY-MLC. In the line of the decisions of the General Assembly and the Church Council the MY-MLC started the Master of Arts Program in Organizational Leadership in 2014.