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There is an increasing burden of neurodevelopmental disorders worldwide, with scarce data in low and middle-income countries, including Nigeria. Little is known about Fragile X disorders (Fragile X syndrome and Fragile X premutation-associated conditions) in developing countries and there is no national data in Nigeria. Advancing Mental Health and Well-being of Nigerian Children Through Public Health Screening for Fragile X Disorders (CHAMP-FX) is a multicentre public health screening initiative designed to estimate the prevalence of Fragile X disorders among children with neurodevelopmental disorders in Nigeria through targeted screening, strengthen diagnostic capacity and provide pathways to targeted treatments. This is a prospective multicentre screening study with longitudinal follow-up recruiting children aged 1-18 years with intellectual disability, autism spectrum disorder, and/or global developmental delay from six tertiary hospitals across Nigeria's six geopolitical zones. Using purposive sampling, 102 participants (17 per zone) will be enrolled. Sociodemographic data and clinical evaluation will be obtained using KoboToolbox. Blood samples will be collected as dried spots on quick-response coded filter cards, stored with desiccant, and transported to the coordinating molecular laboratory. Genetic testing will be performed using a long-range amplification workflow followed by long-read sequencing to determine repeat sizes and classify results using internationally accepted thresholds. The primary outcome is the proportion of participants with Fragile X full mutation and/or premutation in the selected cohort. Secondary outcomes include the distribution of repeat sizes and associations with sociodemographic and clinical variables. Screen-positive participants will receive structured result disclosure, genetic counselling, and referral for appropriate supportive interventions, with targeted therapy using metformin offered to participants diagnosed with Fragile X syndrome. Findings will be disseminated through peer-reviewed publication, conferences and stakeholder engagement.