Abstract: Organizations are challenged to achieve effective and competent results, rising to imminent importance of measuring the performance efficiency. Data Envelopment Analysis (DEA) is an approach that measures performance efficiency of organizations. It is a non-parametric method, which uses linear programming to calculate efficiency in a given set of decision-making units (DMUs). It has widespread application in identifying efficiency and discovering benchmark. In the study, it utilized DEA in identifying School-Based Management (SBM) performance efficiency of one (1) division comprising of elementary and secondary schools - under Department of Education (DepEd) in the Philippines. Efficient schools were used as benchmark for improvement of inefficient schools. The schools had also undergone clustering, which is the process of grouping in accordance to similar characteristics. K-Means clustering algorithm was used to group the schools according to their respective profile. K-Means clustering is a simple unsupervised learning algorithm that follows a simple procedure of classifying a given data set into a number of clusters. The study also encompasses the development of an application system that utilizes data from DEA and K-Means clustering algorithm. The application system also provided recommendations to help inefficient schools improve.