This article explores the perception of gender inequality in science and the influencing factors. Data was collected through in-depth interviews with students belonging to a science club; we present it as a case study. This research sheds light on what high school and university students studying Science, Technology, Engineering, and Mathematics (STEM) perceive in Mexico, where the gender gap is the highest of all scientific disciplines, considering the relationship between science and gender through their study experiences and perspectives. The findings mainly revealed two positions: (1) denial of gender inequalities; and (2) recognition of gender inequalities associated with biological, psychological, and social factors. It is precisely this last factor that is based on a feminist position. How students define and label inequalities varies according to their participation in previous formative experiences linked to gender and contextual influences. Science education activities with a gender perspective are necessary in non-formal education spaces such as science clubs. In this sense, this work offers recommendations that can stimulate the design of training actions for a better-balanced integration of science and gender.