The incidence of congenital hypothyroidism (CH) has increased worldwide over the last decades mainly due to the lowering of screening thresholds, resulting in an increased identification of newborns with transient CH. Several studies reported the prevalence and the predictive parameters of transient CH but reports on the long-term outcome are rare. This study aimed to assess the long-term course of neonates with transient CH. Neonates diagnosed with transient and permanent CH between the years 1998 to 2018 at the Pediatric Endocrine Institute of Ha'Emek Medical Center were enrolled in the study. Data were retrieved retrospectively from medical files. Included in the study were 76 newborns (45M,59%) with transient CH and 53 (25M,47%) with permanent CH. The major cause of transient CH was prematurity (29%) and subclinical hypothyroidism (30%). During retrospective follow-ups of up to 23 years, reinitiation of LT4 therapy was not required apart from four patients with underlying syndromic etiologies. Neurodevelopmental impairment occurred in 16% of children with transient CH compared with 29.4% in the permanent CH group. Transient CH is frequent among preterm infants but is limited to infancy. SCH frequently presents as overt hypothyroidism at birth but in most cases the requirement for LT4 supplemental therapy is limited to the first years of life, suggesting that long-term follow-up of thyroid function tests may be unnecessary for non-syndromic children. The high rate of neurodevelopmental impairment in newborns with transient CH emphasizes the need for neurodevelopmental monitoring in these patients.