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Introduction Anaemia remains a major public health concern among Indian adolescents, particularly girls. National-level and state-level initiatives led by the Government of India, such as the Weekly Iron and Folic Acid Supplementation, Anaemia Mukt Bharat and the Intensified National Iron Plus Initiative, aim to control iron-deficiency anaemia through systematic supplementation and behaviour change communication strategies. However, implementation challenges persist. Given the limited evidence on barriers, facilitators and interventions implemented to improve the outlined national schemes, we have designed a systematic review to inform future research and programmes. This review aims to systematically identify and synthesise evidence on barriers and facilitators influencing the implementation of national iron and folic acid supplementation programmes targeting adolescents aged 10–19 years in India.Methods and analysis A comprehensive search will be conducted using five databases, namely PubMed, EMBASE, Web of Science, CINHAL and Scopus, from inception to 30 September 2025. To capture grey literature, we will also search government portals, international agency repositories, clinical trial registries and the Google platform. Eligible studies include experimental, observational, qualitative and implementation research conducted in school-based, community-based or combined delivery settings. Screening, data extraction and quality appraisal will be performed independently by two reviewers using the Covidence platform. The Joanna Briggs Institute tool will be used to assess methodological quality of included studies. Quantitative data will be synthesised descriptively following the Synthesis Without Meta-analysis guidelines, and qualitative data will be analysed using thematic synthesis.Ethics and dissemination Ethical approval is not required as there is no human participation. The results will be published in a peer-reviewed journal and presented at scientific conferences.PROSPERO registration number CRD420251153248.