Physical education during adolescence, supported by evidenced-based methodologies, offers many different opportunities to practice structured physical activity and promote the development of motor skills, motor coordination, and conditioning. The present study aimed to assess differences in the levels of physical activity, enjoyment, and self-perception in a sample (n = 1029, M = 505, F = 524) of 11–12-year-old secondary schoolchildren according to gender and BMI and determine (a) the mediation effects of physical self-perception in the association between BMI and physical activity and (b) the role of enjoyment in mediating the relation between physical self-perception and physical activity. As part of the Regional Observatory of Motor Development Project (Apulia, Southern Italy), the assessment involved three questionnaires for physical activity levels (PAL), physical self-perception (PSP_C), and enjoyment (PACES). The results showed significant differences in PSP between normal-weight, overweight, and obese children (especially in girls), while there were no significant differences in enjoyment. Physical self-perception partially mediates the relationship between BMI and PAL (R2 = 7.94% for males, 95% C.I.: −0.013, −0.004; R2 = 14.70% for females, 95% C.I.: −0.25, −0.009), and the enjoyment partially mediates the relationship between physical self-perception and PAL (R2 = 6.83% for males, 95% C.I. = 0.003, 0.012; R2 = 13.45% for females, 95% C.I. = 0.002, 0.014). However, only a small percentage of variance was explained, precluding the extension and generalization of the results obtained.