COVID-19 pandemic has increased social media engagement globally. This study examined the correlation between social media use and physical/mental health among university students, considering gender and academic year. Out of 146 responses, 119 were analyzed after excluding participants with pre-existing psychological conditions. Results showed a significant correlation between social media use and mental health for all participants (correlation coefficient = 0.30, p < 0.001), indicating a negative impact on mental health with increased use. Gender-specific analysis revealed a non-significant correlation among males (p = 0.21), while females exhibited a significant correlation (correlation coefficient = 0.32, p = 0.01), suggesting an adverse effect on their mental health. Regarding physical health, females displayed an even higher correlation (correlation coefficient = 0.40, p < 0.001), highlighting the negative influence of social media on their physical well-being. Conversely, no significant correlation was observed among males. Analyzing by academic year, both pre-clerkship and clerkship students showed a significant correlation between social media use and mental health (correlation coefficients of 0.26, p = 0.01, and 0.42, p = 0.03, respectively). Similarly, a significant correlation was found between social media use and physical health among pre-clerkship students (correlation coefficient = 0.34, p = 0.001), but not among clerkship students. In conclusion, this study provides evidence of the adverse impact of social media use on physical and mental health among university students, particularly among females and across different academic years. These findings underscore the importance of promoting healthy social media habits and raising awareness about the potential negative effects on well-being.