Objectives: In 2015, the Iranian Ministry of Health and Medical Education (MoHME) developed and introduced an operational plan (OP) mandatory for implementation for all medical sciences universities. Through this program, a set of indicators were defined for the annual assessment of the universities’ performance. This study examined the effect of OP implementation on universities’ performance and the healthcare system. Methods: We compared seven key performance indicators before and after OP implementation related to public health, education, research, nursing, treatment, food and drug and student affairs. Descriptive statistics, paired t-tests and Wilcoxon tests were used for data analyses using SPSS 26. Results: Of 32 studied indicators, ten indicators were not affected by the OP. Of 22 indicators, including public health (7 indicators), education (2 indicators), research (2 indicators), nursing (5 indicators), treatment (1 indicator), food and drugs (4 indicators), and student (1 indicator) that changed, 17 have improved. Conclusion: OP implementation reached some of its intended goals. The existing OP program process should be replaced with evidence-informed health policies and programs to achieve significant changes in health system functioning and overall public health.
