This study aims to develop a human resource (HR) empowerment model in pesantren-based schools with a soft system methodology approach in Indonesia. The design of this research is development research. The research respondents were 246 people comprising principals, teachers, and staff at three pesantren-based schools in Indonesia. Data collection techniques used were interviews, Focus Group Discussion (FGD), and questionnaires. Data were analyzed with qualitative and quantitative approaches. Qualitative data (interviews and FGDs) were analyzed with the following steps: data collection, data condensation, data presentation, and conclusion. At the same time, quantitative data (questionnaire) was analyzed by descriptive and regression analysis. The results of the research (first and second year) presented a model of human resource empowerment in pesantren-based schools with a soft system methodology approach. In addition, based on the results of data analysis (third year), the model developed had an impact on six variables when implemented. The regression analysis of the six variables concluded that there was a significant influence of instructional leadership, change leadership, spiritual leadership, school culture, and professional ethics on teacher teaching performance.