This study aimed to develop a method for prioritizing resource allocation at universities based on the results of measuring resource efficiency and the market position of study programs. The efficiency was measured using the Data Envelopment Analysis (DEA) method followed by mapping market position of the study program using growth-share matrix (Boston Consulting Group/BCG) and the GE McKinsey matrix. Those methods were combined to create a priority order for allocating organization resources. The objects of this research were 12 undergraduate programs as Decision Making Unit (DMU) at the Engineering Faculty of Diponegoro University. The efficiency measurement result showed that five departments were inefficient, which were Civil Engineering, Urban and Regional Planning, Electrical Engineering, and Geodetic Engineering. Based on market position mapping results, Industrial Engineering and Urban and Regional Planning were categorized as stars. Computer Engineering, Environmental Engineering, Electrical Engineering, Mechanical Engineering, and Geodesy Engineering were classified as question mark categories. The remaining department, Geological Engineering, and Marine Engineering were denoted by lose category. The integration of the DEA method with BCG and GE McKinsey matrix to determine resource allocation matrix based on efficiency and market position was the scientific contribution of this study. The research was conducted based on a business perspective, with the university as a profit institution and the study program as a business unit. This research is intriguing because the indicators used to measure efficiency in a higher education institution are very different from those of a business organization.