Physical self-perception is often related with better physical fitness perception in adolescents. Moreover, it is an important social cognitive perspective to provide suitable mental health in this population. However, this relationship is unequal between boys and girls. The physical fitness is a marker of health in young population. The aims of the present study were the following: (1) to compare physical self-perception and self-reported overall physical fitness (OPF) between boys and girls (gender) and body mass index (BMI) status, and (2) to determine the mediating role of all physical self-perception subscales (except physical condition) and BMI status in the link between gender and OPF in adolescent students. This cross-sectional study consisted of 85 adolescent students of secondary school between 12 and 17 years of age; 41 were boys (M = 14.6, SD = 1.7) and 44 were girls (M = 14.4, SD = 1.6). Adolescent participants completed all clinical characteristics by body composition measures (age, body weight, body height, and BMI). Physical self-perception was assessed by the physical self-perception profile (PSPP) whereas the international fitness scale (IFIS) was used to predict the self-reported OPF of adolescents in the present study. Gender (boys and girls) differed significantly in all PSPP subscales and OPF, whereas the BMI status (underweight = 19 students, normal weight = 53 students, overweight/obese = 13 students) showed significant differences in all clinical characteristics, physical condition (PSPP), and OPF. A multiple mediation analysis was performed using bias corrected bootstrap. This multiple mediation analysis revealed that all PSPP subscales were significant mediators between gender and OPF: attractive body ( = 0.013), sport competence ( = 0.009), physical strength ( = 0.002), and self-confidence ( = 0.002). The total direct effect of gender on OPF was significant ( = 0.002). Moreover, the multiple mediation estimated a completely standardized indirect of X on Y for attractive body (effect = 0.109), sport competence (effect = 0.066), physical strength (effect = 0.130), and self-confidence (effect = 0.193). These findings contribute to understanding the link between gender and OPF in adolescent students and the mediation of physical self-perception and OPF in this relationship. In addition, strategies focused to improve self-confidence and physical self-perception are necessary in female adolescent students, because boys showed better physical self-perception in all PSPP subscales. Girls are a risk group because they report low physical self-confidence with their respective insecurity feelings and psychological disorders. Thus, personal physical self-perception must be considered as an important social cognitive perspective to provide suitable mental health in children and adolescents.