Performance Based Budgeting carried out in Indonesian private higher education found lots of constraints. Apart from factors of cultural work, leadership, and negative perceptions of the community academics, obstacles, and budget limitations are big challenges. This study examines field data related challenge of performance-based budgeting in Indonesian private higher education in particular linked with budget limitations. This study uses a quantitative method with an equipped open questionnaire for getting input about the implementation of performance-based budgeting that is recommended in finance management finance in Indonesian private higher education. Respondents were heads of financial management at 213 private universities in Indonesia. Statistical results show that budget limitations have a significant negative effect on performance-based budgeting in terms of performance orientation of -0.824, implementation flexibility of -0.634, and functional approach of -0.654. Furthermore, proposal optimization of performance-based budgeting with challenging Budget limitations is discussed.