Formative research is an important first step in the design and development of children’s school-based physical activity (PA) interventions. Exploration of educator [headteacher and physical education (PE)-co-ordinator] perceptions toward the promotion of school-based PA, including PE delivery has however been limited. This study took a socio-ecological approach to explore the barriers and facilitators of children’s school-based PA from the perspective of school educators. Interviews were conducted with headteachers (n = 4), PE-co-ordinators (n = 4) and a deputy headteacher (n = 1) and data thematically analysed using Nvivo software (version 10). Findings suggested that, at an organizational level headteachers were the predominant driving force in the promotion of PA opportunities, yet institutional barriers including low priority for PA and PE were perceived to negate delivery. At an interpersonal level, strategies to increase the delivery of school-based PA were developed, however poor teacher-coach relationships and significant others reduced PA promotion opportunities. Child PA was further negated through intrapersonal factors, including lack of PE-specific teacher training and varying teacher interest in PA and sport. To increase primary school children’s school-based PA, barriers and facilitators at the organizational, interpersonal and intrapersonal level must be considered and targeted and researchers and schools should work in partnership to develop future interventions.