Hypomagnesemia 1 (HOMG1) is an extremely rare disease with autosomal recessive inheritance that is caused by mutations in the transient receptor potential melastatin 6 gene (TRPM6). Here, we describe a pediatric HOMG1 case with novel compound heterozygous mutations of TRPM6 (c.1483 C > T [p.Gln495*] and c.2715del [p.Trp905*]) in a 2-month-old boy who developed refractory seizures due to hypomagnesemia with secondary hypocalcemia.