Abstract. This study aimed to: 1) investigate and analyze the implementation of performance-based budgeting system in the Regional Secretariat of Wakatobi District: 2) analyze the organizational effectiveness in the Regional Secretariat of Wakatobi District. Object of the study was the Regional Secretariat of Wakatobi District. Population of the study was all staff at the Regional Secretariat of Wakatobi regency. Informants are determined through purposive sampling method using the following criteria: 1) knowing about the policy of involvement in performance of performance-based budgeting; 2) knowing about the policy of performance-based budgeting; 3) directly involved in the implementation of performance-based budgeting. Data were collected using interview and documentation methods. Data from the research were analyzed descriptively and qualitatively. Results infected that: 1) the application of performance-based budgeting in the Regional Secretariat of Wakatobi District has been done in consistently in accordance with the central government's rules and the Ministry of Finance's regulation, which encompasses everything from determining vision and mission, determining programs and activities , Formulating performance indicators, determining cost standards, activity spending, and making reports; 2) the performance achievement in the Regional Secretariat of Wakatobi District has been very effective.