Background Vehicular use for school journeys contribute to reduced levels of physical activity and social/ environmental interaction in school children, and present significant health concerns across the Western world. Automobile-dependence for these short daily trips is environmentally unsustainable and a major cause of congestion throughout local streets. Significant efforts have been made to enable active modes (e.g., walking and cycling) for travelling to/from school. For a policy or program to be effective, the engagement of many diverse stakeholders is imperative. Although important, the challenges faced by stakeholders relating to school travel remain largely understudied. This research addresses this gap by identifying key challenges that municipalities must navigate when developing and implementing active school travel-related programs and policy. Methods This research was undertaken as part of a larger project that explores potential for cross-jurisdictional coordination in school travel planning. A qualitative investigation was conducted in five municipalities that have implemented active and sustainable school transportation initiatives within the Greater Toronto and Hamilton Region, Canada. Recruitment was facilitated by Green Communities Canada, a not-for-profit organization that has extensive experience in working with these stakeholders. Seventeen participants took part in semi-structured interviews. Participants from various sectors, namely- land use planning, public health, school boards, not-for-profit groups, and law enforcement, were selected based on their level of involvement with current planning process. Results Thematic analysis of interview data revealed five distinct challenges that stakeholders confront, relating to Cross-Jurisdictional Planning, Parent Engagement, Data Collection and Availability, Involvement of Elected Officials, and the Multidisciplinary Nature of Stakeholder Groups. Further, this research identified the ways in which stakeholders have attempted to overcome challenges – offering insights into where additional resources, capacity-building, and improved planning procedures could be introduced. Conclusions This research begins to untangle the intricacies of integrating school travel programs into professional practice, investigating gaps in coordination and obstacles that hinder effective implementation. Identifying and overcoming these challenges are pivotal to the success of future innovative and collaborative transportation planning focusing on children’s health and wellbeing.