Background <p>Neonatal Hypophosphatasia is a rare condition attributed to loss of function mutations in the ALPL gene, resulting in diminished activity of Tissue Non-Specific Alkaline Phosphatase (TNSALP). While it can manifest at various life stages, neonatal onset is particularly ominous, often leading to fatal outcomes. The syndrome’s diverse clinical manifestations pose a diagnostic challenge, necessitating a meticulous approach to rule out other differentials.</p> Case presentation <p>In our case, the observation of neonate’s anomalous posture prompted a comprehensive diagnostic evaluation, including imaging studies. The results of the babygram raised concerns about a potential metabolic bone disorder, leading to a thorough investigation of alkaline phosphate levels. Persistent low levels further raised suspicion for Hypophosphatasia. We provided supportive treatment to the patient which included ventilator support, anti-epileptics for seizures, initially fluids later feed optimization with low calcium formula, vitamin D restriction, and gentle handling along with antibiotics for existing infection. Genetic testing was subsequently performed, confirming the presence of a loss of function mutation in the ALPL gene.</p> Conclusion <p>Our case highlights the significance of astute clinical observation, imaging studies, and biochemical assessments in unveiling this rare disorder. Early identification through a systematic approach allows for timely initiation of treatment, potentially ameliorating outcomes. By elucidating the disease’s symptoms, this case contributes to a better understanding of its natural history, emphasizing the imperative for early intervention to enhance patient prognosis.</p>