Background: Congenital hypothyroidism (CH) is the leading cause of preventable physical and intellectual disabilities. This study aimed to assess the incidence and clinical characteristics of CH in newborns. Methods: We retrospectively reviewed the medical records of all newborns delivered at the Pusan National University Hospital between January 2011 and March 2021. The incidence of CH was compared according to gestational age, birth weight, and small for gestational age (SGA). The patients aged ≥3 years who could not maintain normal thyroid function and required levothyroxine treatment were diagnosed with permanent CH. Logistic regression analysis was performed to compare CH risks. Results: Of 3,722 newborns, 40 were diagnosed with CH (1.07%). Gestational age and birth weight were significantly associated with CH incidence. The odds ratios (ORs) of CH in infants delivered at 32-37, 28-31, and <28 weeks were 2.568 (95% confidence interval [CI], 1.141-5.778), 5.917 (95% CI, 2.264-15.464), and 7.441 (95% CI, 2.617-21.159) times higher, respectively, than those delivered at term. The ORs of CH in infants weighing 1,500-2,499 g, 1,000-1,499 g, and <1,000 g were 4.664 (95% CI, 1.928-11.279), 11.076 (95% CI, 4.089-29.999), and 12.544 (95% CI, 4.350-36.176) times greater, respectively, than those in infants weighing ≥2,500 g. The OR of CH was 6.795 (95% CI, 3.553-13.692) times greater in SGA than in non-SGA infants. Conclusion: The CH incidence in South Korea has increased significantly compared with that in the past. Gestational age, birth weight, and SGA were significantly associated with CH incidence.