We present a case of a 1-year-old female child who was referred to the Early Intervention Clinic for evaluation of developmental delay and progressively enlarging head size. Developmental assessment revealed significant motor delay with borderline cognitive impairment. MRI of the brain revealed generalized ventriculomegaly secondary to narrowing of the spinal canal at the cervicomedullary junction. Targeted array-based comparative genomic hybridization showed deletion of approximately 602 kbp from band p12.2 region of the short arm of chromosome 16, which encompasses 16p12.1 microdeletion syndrome. The 16p12.1 microdeletion syndrome has been recently recognized as an important contributor of developmental delay and other neuropsychiatric phenotypes in the child. To date, no case of cervicomedullary spinal canal stenosis with hydrocephalus has been reported with 16p12.1 microdeletion syndrome.