Menkes disease is an X-linked recessive condition caused by mutations in the gene, which leads to severe copper deficiency. Aminoacylase-1 deficiency is a rare inborn error of metabolism caused by homozygous or compound heterozygous variant in the gene, characterized by increased urinary excretion of specific N-acetyl amino acids. We report an infant with neurological findings such as seizures, neurodevelopmental delay and hypotonia. Metabolic screening showed low serum copper and ceruloplasmin, and increased urinary excretion of several N-acetylated amino acids. Whole-exome sequencing analysis (WES) revealed the novel variant c.3642_3649dup (p.Ala1217Aspfs*2) in the gene, leading to a diagnosis of Menkes disease, and the simultaneous presence of the homozygous variant c.1057C>T (p.Arg353Cys) causative of Aminoacylase-1 deficiency. Our patient had two rare conditions with different treatment courses but overlapping clinical features. The identified novel mutation associated with Menkes disease expands the gene spectrum.