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Today, paying attention to innovation in achieving economic growth and development is of great importance for researchers and policymakers. Thus, this study investigates the efficiency of the national innovation system of Iran in comparison with the countries subject to the 2046 Vision of Iran as well as China and South Korea (as two successful countries in technology catching-up policies). The study uses a two-stage Data Envelopment Analysis (DEA) over the period 2011-2016. Moreover, a Tobit model is employed to study the impact of environmental factors on the efficiency of the national innovation system. Findings indicate that Iran's national innovation system is inefficient. Although the efficiency trend in the stage of creating inventions and originalities shows a positive slope, when it enters the commercialization stage, the system operates very weekly. To increase the efficiency of the national innovation system, improving the governance indicators and university-industry collaboration are among the most effective policies proposed in this research.