The aim of national education in Indonesia is to give a great quality of education for all people. E-learning system's evaluation has become critical to fulfilling this situation. The purpose of this study is to consolidate the multi-dimensional aspects of e-learning evaluation by applying Balance Scorecard (BSC) as a strategic measurement method. This study further seeks a solution for designing a systematic approach in which three equally important considerations must be balanced; organization, pedagogical, and technology. To identify measures of each perspective, this research conducted a comprehensive literature review and using survey analysis. This research is introducing a framework for assessing e-learning system using the fuzzy analytic hierarchy process (FAHP) and BSC, the result proposes integrating pedagogical, organizational, and technical measures based on the BSC framework.