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Factor X (FX) deficiency is an extremely rare inherited bleeding disorder affecting one in 1,000,000 people. According to the most recent published census of the World Hemophilia Federation, to date there is no reported case of FX deficiency in the Philippines. Rare disorders like FX deficiency often go unrecognised or misdiagnosed. Here, we report the first case of FX deficiency in a Filipino child. A two-month-old male child with consanguinity was referred to our hospital due to bleeding episodes. On the third day of life, he had haematomas to the cervical area and upper extremities, and spontaneous bleeding of the umbilical cord was noted. Initial workup showed prolonged PT and aPTT. Factor deficiencies including FVIII and FIX were considered, however assays were normal. At six weeks of age, the child developed convulsions and deteriorating neurologic status. CT scan showed subarachnoid haemorrhage. The child was referred for further workup. Additional assay of clotting factors showed decreased FX activity at less than 1% and he was diagnosed with severe congenital FX deficiency. Following recurrent intracranial bleeding, the child has been observed to have permanent neurological deficit. This case highlights the importance of timely and accurate diagnosis to prevent life-threatening complications and the risk of permanent disability. Despite being an extremely rare disorder, the incidence of FX deficiency is estimated to be higher in populations where consanguineous marriages are common. Awareness of this rare condition must be emphasised. Families may benefit from screening through coagulation studies as well as genetic counselling, especially when planning future pregnancies. The rarity of this condition has not allowed for the establishment of evidence-based management guidelines, with treatment based on limited literature. Despite development of FX-specific clotting factor products, the high cost and limited availability impact their use in low-resource settings.