The health system uncertainty index is a key metric for assessing the stability and resilience of a health system and the extent to which it is affected by economic shocks and health crises. This study estimates a health system uncertainty index for Iran over the period 1989–2024 using GARCH models. Health-related uncertainty refers to the volatility and unpredictability of indicators associated with public health and the health economy, which can influence decision-making by households, the government, and investors in the health sector. To this end, four main sub-indices were selected: (1) child mortality and child health, (2) access to services and vaccination, (3) public health and safety, and (4) health economic indicators and life expectancy. A composite uncertainty index was then constructed by taking the standardized average of these sub-indices. The results show that health uncertainty in Iran followed an overall downward but volatile trend during the study period: the index was close to 0.9 in the late 1980s and declined to around 0.15 by the mid-2010s. However, since 2019, the index has increased again due to financial sanctions, budget volatility, and the outbreak of COVID-19. An analysis of the GARCH coefficients indicates that the child mortality and child health sub-index accounts for the largest share of fluctuations in uncertainty, while access to services and vaccination exhibits the greatest stability. Overall, the findings highlight the high sensitivity of health outcomes to economic instability and institutional weaknesses in health financing. Therefore, establishing sustainable financing mechanisms, strengthening institutional transparency, and expanding health insurance coverage can help reduce uncertainty and enhance the resilience of Iran’s health system.