Hypomagnesemia is a rare cause of seizures in childhood. But should be in mind in recurrent and intractable seizures and hypocalcemia the communities where consanguineous marriages are common. Familial hypomagnesemia with secondary hypocalcemia is a rare genetic cause of hypomagnesemia due to the variant in the transient receptor potential melastatin 6 genes. Here, a 3 year-old boy who has been identified a novel variant in this gene and had difficulties in enteral hypomagnesemia treatment was presented.We presented a 3 year-old boy having recurrent seizures since 2 years old and diagnosed as epilepsy and treated with multiple antiepileptic drugs. But then, he was diagnosed as rickets due to severe hypocalcemia an outer center. The patient was hypotonic and neurodevelopmentally poor. Our prominent laboratory finding was hypomagnesemia with secondary hypocalcemia. The genetic analysis revealed a novel variant in transient receptor potential melastatin 6 gene. After the parental treatment of intravenous magnesium sulfate and calcium, the treatment was switched to enteral magnesium medications. Because of persistent hypomagnesemia and the gastrointestinal side-effects, different oral preparations were used. The patient was stable on an oral maintenance dose of magnesium oxide with borderline blood magnesium levels without hypocalcemia.Hypomagnesemia is one of the causes of hypocalcemia. Enteral replacement is the key in the treatment but the treatment should be individualized for each patient. Normalization of hypomagnesemia is not always easy and should not be the aim of the treatment.