A Public Service Agency, known by the Indonesian nomenclature as Badan Layanan Umum (BLU), is a government institution with the autonomy to manage its finances effectively and efficiently and provide public services. BLU is crucial for delivering essential services in Indonesia, including specialized education in the transportation sector. Despite their significance, BLU institutions like the Indonesian Civil Pilot Academy Banyuwangi face operational inefficiencies, financial constraints, and human resource challenges that hinder organizational performance. This study investigates these challenges, focusing on how financial management, human resource issues, and operational inefficiencies affect educational outcomes. The research employed a qualitative case study approach using semi-structured interviews, document analysis, and field observations. Data were collected from key stakeholders, including students, lecturers, and staff, to assess organizational performance in the educational process, human resource management, and general operations. Findings reveal that while facilities and educator engagement have improved, issues such as lecturer absenteeism, student input quality, and the need for continuous staff training persist. This study contributes to the body of knowledge by demonstrating the critical role of Total Quality Management (TQM) and Cross-Functional Integration (CFI) in improving public service agency performance. The research offers practical recommendations for enhancing lecturer performance, refining student admissions, and developing powerful individuals through sustainable training. This expectation can give Public Service Agency management an outlook for increasing performance organization and support mission, as well as the Agency of Human Resources Development (BPSDM) on Transportation vision.