This study quantifies the long-term impact of the 1979 Iranian Revolution on Iran’s trajectory of scientific publications, a critical examination for science and public policy. Using comprehensive data from 1960 to 2024, we benchmark Iran against pre-revolutionary peers (e.g., South Korea) and employ multidimensional scientometrics, including the rigorous Synthetic Control Method (SCM). Results demonstrate a significant divergence: Iran, which led its peers in 1978, experienced collapse and stagnation (1980–1999) while peers grew exponentially. SCM, which optimally matches pre-1979 Iran with South Korea, quantifies a cumulative knowledge deficit of approximately 551,000 publications by 2024. Furthermore, despite a post-2000 volume recovery, a persistent quality gap exists; research impact (measured by Field-Weighted Citation Impact) consistently lags behind the global average. This analysis provides a robust, data-driven quantification of the generational opportunity cost of the 1979 disruption on national scientific development.