Background: Neonatal hypocalcemia is a metabolic abnormality commonly reported. Late onset hypocalcemia usually manifests after 7 days and requires a long-term therapy. Neonatal hypocalcemia due to hypoparathyroidism can manifest as life-threatening seizures or tetany. Initial management is important to prevent any complication due to this condition. However, the initial management to correct hypocalcemia with the administration of calcitriol, high dose intravenous and oral calcium may take longer to achieve because of hypoparathyroidism. Case summary: We report a case of late onset neonatal hypocalcemia in a nine-days-old baby. He was born on the 35-36 week of gestational age by Caesarean section, without asphyxia nor neonatal infection. The baby had a refractory seizure with low serum calcium and magnesium, high phosphate, normal alkaline phosphatase (ALP) and low calcium creatinine urine ratio. His 25-hidroxy vitamin D (25-OHD) total was as low as 12.9 ng/mL. And, he has a low level of parathyroid hormone (PTH). Adequate correction for hypocalcemia and hypomagnesemia failed to maintain calcium and magnesium to their normal value. Oral calcium gluconolactate and carbonate were added after calcitriol supplementation, but seizure still noticed. After magnesium oxide supplementation was given, another seizure had never occurred. A long-term follow-up on vitamin D and calcium level were required. Conclusion: In a hypocalcemic newborn patient, assessment of the magnesium, vitamin D, and PTH status are needed.