Objective: To determine the gender-based variation in the academic performance of medical students. Methodology: This cross-sectional was carried out from January to February 2023. The students were taught two Physiology and two anatomy lectures, then after a month, the theory BCQs test of a total of 150 marks and viva-voce and OSPE of 150 marks (Total 300 marks) from the same taught topics, was conducted. The gender-based difference in the grade of students was tested using the Chi-Square test. Data analysis was done using IBM SPSS version 23.0. Results: Among (n=290) students, 117(40.34%) were male students while 173(56.66%) were the female students. Among the 117 male students, the mean±sd of total marks was 164.8 ±38.67 out of a total of 300 marks, while among the 173 female students, the mean±sd of total marks was 181.50±30.90 out of a total of 300 marks. There was a statistically significant difference in the score of students based on gender (p<0.01). Conclusion: According to this study's findings, there was notable gender discrepancies among undergraduates and female students performed much better academically than male students, as indicated by the cumulative grade point average they earned at the university. There was a statistically significant difference in the score of students based on gender (p<0.01).