<p>This study addresses the persistent challenge of developing performance management systems (PMS) in public sector organizations that effectively align strategic goals with operational outcomes. While conventional approaches often struggle to accommodate the complexity and dynamics of public administration, the potential of systems thinking to bridge this gap remains underexplored. Focusing on Indonesia’s National Directorate of Post and Informatics Resources (NDPIR), this research applies a systems thinking perspective to enhance performance management. Using Soft Systems Methodology (SSM) and multiple data collection techniques, the study develops an integrated PMS that connects strategic planning with operational execution. The framework incorporates the Balanced Scorecard (BSC) to structure and validate Key Performance Indicators (KPIs), ensuring alignment across organizational layers. Six KPIs were established with defined baselines, targets, measurement methods, and departmental responsibilities. The methodological contribution lies in integrating SSM and BSC within a complex governmental setting to foster stakeholder engagement, strengthen organizational learning, and develop actionable metrics. This approach contributes to systems thinking applications in the public sector by demonstrating how participatory methods can be combined with structured performance models to promote accountability, transparency, and continuous improvement in governance.</p><p>Clinical trial number: Not applicable.</p>