This complete enumeration, cross-sectional comparative study was conducted in the Physiology Department of a municipal medical college in Maharashtra, India to determine the gender differences in scores obtained by students in objective structured practical examination. After explaining the purpose of the study and the procedure of the Objective Structured Practical Examination to first-year MBBS students (n=60; 30 females and 30 males), written informed consent was obtained. The examiners were provided with a pre-validated checklist for assessing the students’ performance at the procedure station. After the procedure station, the students shifted to the question station for writing answers to ten short-answer type questions. The overall mean score (out of 20) in the procedure station was 18.57  1.88 (95% CI: 18.09–19.04) while the mean score in the question station (out of 20) was 10.98  4.05 (95% CI: 9.96–12.01). The gender differences in mean scores were not significant (p=0.499) at the procedure station that primarily assessed the psychomotor domain at the “shows how” level of the Miller’s Pyramid. However, male students obtained significantly (p=0.015) lower mean scores at the question station that chiefly evaluated the cognitive domain at the “knows” and “knows how” levels. This implied that while both male and female students were equally proficient at performing the procedure (psychomotor domain) component of the practical, the male students were deficient in the knowledge (cognitive domain) component of the practical, when compared with their female counterparts.