Height gain is a critical indicator of childhood stunting in Ugandan girls' secondary schools. School-based nutrition programmes have been implemented to address this issue, but their effectiveness varies across settings. Qualitative data were collected through interviews with educators, parents, and students from ten randomly selected schools. Focus groups and observation logs provided insights into the programmes’ implementation and impact on stunting. A notable theme emerged regarding the consistent improvement in participants' height measurements over the intervention period, although initial gains varied across different schools due to varying programme adherence and resource availability. While school-based nutrition programmes showed potential as a strategy for combating childhood stunting, their success was contingent upon local context-specific adaptations and sustained support. Schools should tailor nutrition programmes to local needs and resources, while community engagement is crucial for long-term sustainability. Monitoring and evaluation frameworks are essential for continuous improvement and impact assessment.