Introduction: School-based running programs that promote daily (or regular) walking/jogging/running are an emerging public health initiative. However, evaluation of these programs has predominantly used quantitative measures that limit understanding and explanations of contextual influences on pupil participation. Therefore, the aim of this study was to qualitatively explore pupils’ experiences of participating in a primary-school-based running program (Marathon Kids) to provide relevant insights and inform program developments. Methods: Nine semistructured focus groups were conducted with a purposeful sample of 50 pupils (26 girls and 24 boys) between 6 and 10 years of age from 5 primary schools in England. All schools had delivered the running program for 5–9 months during the 2015–16 academic year. Transcripts were analyzed using an inductive thematic approach. Results: Pupils identified a range of organizational, interpersonal, and intrapersonal factors that they believed influenced their participation in the program. Six themes were identified as being important to pupils’ experiences: Marathon Kids as an enabling program, pupils’ autonomy to participate, peer influence on participation (e.g., development of social cohesion), teacher influence on delivery (e.g., fidelity of implementation), logistics and suitability of the school environment, and appropriateness of program resources. Conclusions: School-based running programs can offer an enjoyable physical activity experience for children; however, it is important to understand how current delivery approaches influence pupils’ participation. Aspects that were believed to facilitate enjoyment included pupil autonomy to participate, perceived benefits of participation (including psychosocial outcomes), and a supportive school environment. Further research is required to identify the type and level of support required by schools to sustain pupil participation in running programs so that their perceived value is maintained.