The main objective of this study is to know how gender influences the relationship between 3D depth perception and mental object rotation skills. We conducted standard vision tests and a mental rotation task on 155 participants (78 males, 77 females) aged between 19 to 33. The results recommend that both the genders performed the tasks equally in stereopsis function, but males accuracy was better in mental rotation tasks, particularly during complex 3D depth perception task. The 41% response time (RT) disparity (p < 0.001) and significant accuracy gap recommend that environmental and cognitive factors knowingly control spatial abilities. We suggest that the targeted spatial training could reduce these disparities.