Extra-curricular physical activity (ECPA) may have an important role to play in the health and well-being of adolescents, but the actual benefits are relatively unknown. This study examined ECPA participation amongst adolescent males (age 12-15 years) from disadvantaged backgrounds, and evaluated its impact on overall physical activity (PA) accumulation and psychological well-being. At three time points over a single academic year, participants from four schools (n = 174) wore a pedometer for seven days and completed a questionnaire assessing habitual PA, frequency of ECPA participation, barriers to ECPA participation and seven psychosocial subscales. An average year-long score was calculated for each participant, for each variable. Across seasons, 84% of participants reported regular (= twice a week) or occasional (once a week) participation in ECPA. Those reporting regular participation in ECPA were significantly (p < 0.01) more active (steps/day) and scored higher (p < 0.01) on each psychosocial subscale. Results of multinomial regression analysis showed that perceived physical competence (p < 0.001) had a significant main effect on ECPA participation. Our study results indicate that students from disadvantaged backgrounds whom participate in ECPA at least once a week are significantly more physically active and have a higher level of psychological well-being than those who never participate.