Public University has state ownership and/or receives public funds through a federal/national or subnational government. As the budgetary entity, Public University spends budget money and every citizen demands greater understanding of where their tax money goes and spends. The purpose of this paper is to study performance evaluation of Public Universities complying with Public Sector laws/rules. This paper suggests that the construction process of performance measurement should be aligned with outputs and outcomes of budget policy. Performance evaluation of Public University as a whole organization is considered in the three aspects: design/creating, evaluating, and challenging/monitoring. Subsequently, author aims to investigate the latest achievement in evaluation, monitoring, and challenges for public universities’ KPI system. Texts and contents from different sources such as financial annual reports and budgetary entities’ websites provided insightful and findings. In addition, the research result lightens the most important drawbacks and challenges facing during the public universities performance measurement.