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Understanding the socioeconomic inequalities in the prevalence of non-communicable disease risk factors can facilitate the development of more effective interventions. We aimed to assess the potential socioeconomic inequality in the prevalence of smoking, waterpipe smoking, low fruit and vegetable consumption, hypertension, physical inactivity, and metabolic syndrome among the employees of the Tehran University of Medical Sciences (TUMS). We employed the baseline data of 4,476 individuals who participated in the Tehran University of Medical Sciences employees` cohort study (TEC) (2018–2021). Age-adjusted prevalence was estimated for each risk factor by education level and wealth quintile. We also estimated the absolute and relative socioeconomic inequality in the prevalence of each risk factor using the Slope Index of Inequality (SII) and Relative Index of Inequality (RII), respectively. The analyses were adjusted for gender, age, and marital status, length of employment, and type of employment contract. The highest absolute wealth-related inequality was observed in physical inactivity (38.9%). The age-adjusted prevalence of low fruit and vegetable consumption in the lowest wealth quintile was 18.8% higher than in the highest quintile (SII: 18.8, 95% CI: 13.5 to 24.1, P < 0.001). Moreover, the prevalence of low fruit and vegetable consumption in the lowest wealth quintile was 2.04 times higher than in the highest wealth quintile (adjusted RII: 2.07, 95% CI: 1.50 to 2.82, p < 0.001). Also, the relative education-related inequality analysis showed that after controlling for age, gender, marital status, wealth index, length of employment, and type of employment contract, the prevalence of active heavy smoking in no-formal or primary educated individuals was 9.14 times higher than that in individuals with a doctoral degree education level (adjusted RII: 9.14, 95% CI: 5.13 to 16.22, P < 0.001). The results showed a significant socioeconomic inequality in the prevalence of low fruit and vegetable consumption, metabolic syndrome, and smoking across wealth quintiles. Moreover, education-related inequalities were observed in several major non-communicable disease risk factors.