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Remuneration is one method to encourage individual performance as well as organizational performance. Some studies show organizational performance has structure and policy effects to staff. Narrow down the distinction is needed to ensure such policy on performance working properly. This situation currently happens at the public university as response to organizational and individual performance. This study aims to analyze the implementation and challenges of remuneration on the performance of lecturers at the Mulawarman University. This research uses a descriptive qualitative approach. The method used in qualitative research is conducting semi-structured interviews with several participants and adapted to the study. The results show that there are factors that support and hinder the implementation of remuneration at the Mulawarman University. There are supporting factors, such as regulation, performance guidelines, socialization of procedure, lecturers- performance, policy implementation, human resources, organizational capability, commitment of implementers and evaluation. While, the inhibiting factor are timelines and method used to measure performance. The biggest challenge of this remuneration policy at the Mulawarman University is financial management and adequacy of funding to sustain the implementation of remuneration. In short, to sustain better individual and organizational performance, improvement of business plan and development need to be done quickly.