Objective: To assess the school breakfast program (SBP) in two schools with high Aboriginal student populations in rural Western Australia, their contribution to holistic support, nutritional health education and possibilities for improvement. Methods: The operations and functioning of one regional and one remote SBP were assessed by stakeholder inquiry related to process and challenges, observations and documentary review. An intervention to increase health education, social interaction and learning about nutrition and food origins implemented in one school was assessed. Results: Strengths, system and structural factors that impeded realisation of optimal outcomes of the SBPs were identified. The SBPs focussed on serving food rather than building nutritional understanding or on social interactions and support. Systems for delivery and management of the programs largely relied on staff with limited time. When offered a more interactive and social environment, children enjoyed learning about food. Conclusions: Opportunities for SBPs to offer holistic support and educational enhancement for disadvantaged children are limited by the realities of pressures on staff to support them and a view constraining their primary role as food delivery. The lack of volunteer support in disadvantaged schools limits the potential benefits of SBPs in providing psychosocial support. Health education resources which exist for use in SBPs are not necessarily used.