To study the association between serum magnesium level and migraine in children. This cross-sectional study enrolled children aged 5-18 years diagnosed with migraine, and age- and sex-matched controls without a headache disorder. International Classification of Headache Disorders 3 (ICHD-3) was used for the diagnosis of migraine. The association between serum magnesium level and migraine headache was analyzed. A total of 35 children with migraine were enrolled with 35 control subjects. The median (IQR) serum magnesium levels were comparable among children with migraine and controls [2.0 (2.0,2.1) vs 2.2 (1.9, 2.2) mg/dL; P=0.23], respectively. In adolescent sub-group, median (IQR) serum magnesium levels were significantly low among the children with migraine as compared to those without migraine [2.0 (1.9, 2.1) vs 2.2 (2.0, 2.2 mg/dL); P<0.045]. We found a statistically significant association between low serum magnesium levels and the occurrence of migraine in adolescents, which may have treatment implications.