The weekly iron and folic acid supplementation (WIFAS) programme is a school-based initiative designed to reduce iron and folate deficiency anaemia among adolescent girls. In Ethiopia, donor-supported pilot programmes are implementing WIFAS in schools, but evaluations of its demand- and supply-side barriers and facilitators remain limited. This study aimed to explore these barriers and facilitators in the Sidama Region of Ethiopia. An exploratory qualitative study collected data from ten WIFAS-targeted schools using key informant interviews (KIIs) and focus group discussions (FGDs). Participants included purposively selected school directors, WIFAS-trained teachers, health centre heads, district health and education office nutrition focal points, and regional health and education bureau delegates. Ten FGDs were conducted with adolescent girls and their mothers. Thematic analysis was performed using Open Code software to identify emerging themes. This study identified low awareness of iron and folic acid (IFA) tablets, negative community perceptions, fear of side effects, supplementation interruptions due to school closures, and inadequate coverage as key barriers. Structural barriers included poor programme coordination, weak supply chain management, and water scarcity. Facilitators included free IFA tablet distribution, health extension workers’ involvement in awareness campaigns, positive testimonials, local leader support, training, and regular supervision. The WIFAS programme implemented in schools of the Sidama Region faces programmatic and structural barriers. However, facilitators like free IFA distribution, health extension worker involvement, and community support offer opportunities for improvement. These findings highlight the need for addressing barriers while leveraging existing facilitators for enhancing programme success.