Migraine is a common neurological disorder in developmental age, involving up to 20% of children and adolescents. Although gender differences in migraine epidemiology and clinical characteristics have been largely investigated in adulthood, this issue is considerably less known in pediatric patients. We aim at providing an overview of gender differences in pediatric migraine. The most recent literature was reviewed taking into account the epidemiological, pathophysiological, and clinical differences between boys and girls with migraine. Although many aspects need to undergo further investigation, we conclude that different aspects of childhood migraine syndrome may vary depending on the gender and age, especially with regard to pubertal development.