Strengthening the health systems through gaps identification is necessary to ensure sustainable improvements especially in facing a debilitating outbreak such as COVID-19. This study aims to explore public perspective on health systems' response towards COVID-19, and to identify gaps for health systems strengthening by leveraging on WHO health systems' building blocks. A qualitative study was conducted using open-ended questions survey among public followed by in-depth interviews with key informants. Opinions on Malaysia's health systems response towards COVID-19 were gathered. Data were exported to NVIVO version 12 and analysed using content analysis approach. The study identified various issues on health systems' response towards COVID-19, which were then mapped into health systems' building blocks. The study showed the gaps were embedded among complex interactions between the health systems building blocks. The leadership and governance building block had cross-cutting effects, and all building blocks influenced service deliveries. Understanding the complexities in fostering whole-systems strengthening through a holistic measure in facing an outbreak was paramount. Applying systems thinking in addressing gaps could help addressing the complexity at a macro level, including consideration of how an action implicates other building blocks and approaching the governance effort in a more adaptive manner to develop resilient systems.