Higher education institutions nowadays are moving towards recognizing the importance of knowledge to gain competitive advantage against its rival competitors and the pressure to face globalization. This has been an important issue encounter by many countries, where Malaysia made no exception is aspiring to become a regional education hub in Asia. As societies moving from industrial to knowledge era, knowledge management should also be embedded in education sectors to act as a medium to improve teaching and learning experience. The objective of this paper is to explore the factors affecting the acceptance of knowledge management system in higher education institutions in Malaysia. Due to scarce empirical knowledge about these relationships, the needs for further research in this area is crucial. The results show that only organization culture and organization structure contribute significantly towards knowledge management systems acceptance in Malaysia, compared to individuals factors. The findings highlight the important of organizational learning in the process of managing knowledge in the academic institutions.