We report an infant with XMEN who acquired a novel mutation in the <i>MAGT1</i> gene, presenting recurrent severe skin infections and neutropenia after 6 months of age, which was effectively managed following aggressive anti-infective treatment and HSCT. Here, MAGT1 is linked to X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia.