The purpose of this study is to establish balanced scorecard (BSC) in performance measurement of elementary and secondary schools' MIS Department. We take a broader definition of elementary and secondary schools' MIS Department as “an assembly which brings forth some specific functional activities to fulfill the task of MIS.” BSC used as a measurement tool to assess study subjects, according to its strategy and goal formed by its assignment property, can be divided into four dimensions: finance, customer, inter process, learning and growth, which can provide us with a timely, efficient, flexible, simple, accurate, and highly overall reliable measurement tool. In order to extract the knowledge and experience from related experts to pick out important evaluation criteria and opinion, this study combines fuzzy theory and the analytical hierarchy process (AHP) to calculate the weights. After completing weighted calculation of every dimension and indicator, the BSC model is thus established. The findings of this study show that the indicator weightings between and among all the levels are not the same, rather there exists certain amount of differences. The degrees of attention drawing in order of importance among all dimensions are customer, financial, internal process and learning and growth dimension. After comprehensively analyzing indictors of performance measurement included in every level, the highly valued top five indictors are, when conducting dimension performance measurement in elementary and secondary schools' MIS Department, “Rationalize software and hardware and maintenance expenses,” “Budget satisfy and control,” “Quick response and handling,” “Improve service quality,” and “High effective information system”.