The purpose of this paper is to design a risk-based performance audit program for Comptroller of Supreme Court of Indonesia by analysing the implementation of the existing audit plan process. This research is a qualitative research with descriptive analysis. The paper uses responses from the Comptroller of Supreme Court of Indonesia for analysing the existing audit plan process and uses responses from managers of court fee in five District Courts for analysing the court fee management. We further arrange risk register of court fee management using the audit reports and the responses in focus group discussion with risk owner. The results show that although the Comptroller of the Supreme Court has limited resources, the existing audit plan process doesn't use risk basis as required by the Institute of Internal Auditor (IIA) Standard. Therefore, we propose to use the risk base for designing performance audit program. Specifically, we determine audit topic in periodic planning by scoring potential topics based on macro risk factors. The court fee topic gets the highest score so it is chosen as a performance audit topic. We further prepare the planning of performance audit assignment by analysing the court fee management, including assessing the risks in the District Court. Finally, this research produces a risk-based performance audit program in the face of resource constraints in Comptroller of Supreme Court.