Purpose: This study aimed to investigate the prevalence of delayed thyroid dysfunction based on iodine disinfectant use and to analyze associated risk factors. Methods: A retrospective study was conducted on late preterm infants admitted to the neonatal intensive care unit between January 2010 and June 2018, who underwent neonatal thyroid screening (NTS) and ≥2 thyroid function tests (TFTs). NTS was performed 3 days after birth, with at least two TFTs 1 week and 2 to 4 weeks after birth. To distinguish between normal and dysfunctional thyroid levels, we reviewed TFT results at 2 to 4 weeks and examined possible risk factors for the development of thyroid dysfunction. Results: Of 295 late preterm infants, 262 were enrolled with a mean gestational age and birth weight of 34.8±0.7 weeks and 2,170±454 g, respectively. A total of 7.6% developed hyperthyrotropinemia at the age of 24.3±14.6 days (range, 12 to 69). The incidence of hyperthyrotropinemia during iodine use was approximately 12.6%, while that during discontinuation was 2.4% (P=0.002). Multivariate analysis revealed that small for gestational age (SGA), iodine disinfectant use, and abnormal NTS results were significant risk factors for delayed hyperthyrotropinemia (adjusted odds ratio [AOR]: 4.27, P=0.008; AOR: 8.24, P=0.003; and AOR: 7.80, P=0.002, respectively). Conclusion: Delayed hyperthyrotropinemia was prevalent in late preterm infants exposed to topical iodine and those identified as being SGA. Secondary TFTs should be considered 2 to 4 weeks after birth for this population at risk.