Background: Chromosome 22q11.2 microduplications are extremely rarely detected; in comparison, the deletion of same region, known as the DiGeorge/velocardiofacial syndrome, occurs more frequently. Thyroid anomalies commonly occur in patients with 22q11.2 deletion syndrome, however few reports of thyroid anomalies associated with 22q11.2 microduplication have been published thus far. Case Report: We present a case of a male infant who was prenatally diagnosed with 22q11.2 microduplication and was found to have congenital hypothyroidism due to thyroid hemiagenesis after birth. Moreover, the baby had bilateral hearing impairment, bilateral cryptorchidism, and a rotated penis. At the age of 2 years, the infant was euthyroid with levothyroxine replacement, but he showed significant developmental delay. Conclusions: To our knowledge, this is the first case of congenital hypothyroidism with thyroid hemiagenesis in a patient showing 22q11.2 microduplication. Thyroid dysgenesis could be an additional clinical feature shared by the 22q11.2 microduplication and deletion syndrome, suggesting that the duplication and deletion of a gene may result in a common phenotype. Thyroid dysgenesis should be considered in the evaluation and management of patients with this genomic disorder.