Background: Authorities recommend that youth undertake at least 60 minutes of daily moderate-to-vigorous physical activity (MVPA), with young people having the opportunity to undertake at least half of this MVPA during school hours. Methods: In this study, we examined the influence of school-level socioeconomic status (SES) on children's PA, fitness and fundamental movement skill (FMS) levels, and the barriers and enablers of children's PA in 86 Australian schools (41 primary, 45 secondary). School-level SES was based on an Index of Community Socio-Educational Advantage (ICSEA). School representatives reported potential barriers and enablers for children's PA. We used subjective and objectives measures of PA, fitness, and FMS levels. Multiple logistic regression examined the associations of ICSEA category (low or high) with barriers and enablers, and PA outcomes, adjusting for children's language background and residence. Results: Children from high SES schools were more likely to achieve the healthy fitness zone for cardiorespiratory fitness; those from low SES schools consistently reported more barriers and fewer enablers than their high SES counterparts. Conclusions: Extra efforts may be required to address school-level barriers and enablers to enhance PA, fitness, and FMS levels for schools in disadvantaged areas.