This paper introduces a comprehensive analytical framework for measuring food system resilience in fragile situations, integrating the concepts of resilience and fragility. Our proposed framework defines resilience as structural, institutional, and individual capacities at macro, meso, and micro levels. Fragility is characterized by weak institutional performance and heightened vulnerabilities at the macro level, and operationalized by individual and community perceptions and experiences of fragility at the meso and micro levels. The framework emphasizes a multi-level approach to food systems, clearly distinguishing systemic fragility from individual resilience capacities. It proposes a measurement framework with indicators across economic, environmental and climate, security and social, and political and institutional dimensions. This framework can be implemented empirically with an agile measurement system employing a combination of secondary data (including satellite imagery, event data, and administrative records) and frequent, short-duration primary surveys capturing both objective conditions and subjective experiences in challenging environments. Ultimately, the proposed framework serves as a robust tool to analyze how food systems respond to stressors in fragile situations, providing actionable insights for enhancing resilience.