Microcephaly, a neurodevelopmental condition characterized by reduced head circumference, poses significant challenges for affected children and their families. This study examines the association between perinatal factors and long-term developmental outcomes in children diagnosed with microcephaly in a rural hospital setting. A retrospective cohort analysis was conducted, including clinical records of infants born over a ten-year period. Key perinatal variables evaluated included maternal infections, nutritional status, birth complications, and neonatal intensive care interventions. Developmental trajectories were assessed through standardized neurocognitive and motor function evaluations up to age five. Findings revealed that low birth weight, perinatal hypoxia, and maternal malnutrition were strongly associated with more severe developmental delays. Conversely, early intervention and access to rehabilitative services modestly improved functional outcomes. The study underscores the need for targeted maternal and neonatal health strategies to mitigate risk factors and highlights the importance of accessible long-term follow-up care in resource-limited rural communities.