In Kanagawa Prefecture, Japan, simultaneous measurements of free T4 (FT4) and TSH levels are performed during newborn screening for congenital hypothyroidism (CH). FT4 measurement enables the detection of CH of central origin (CH-C), the incidence of which is estimated to be 1 in 30,833 live births in Kanagawa Prefecture. In this study, we aimed to evaluate the efficacy of FT4 screening when transient CH-C and thyroidal CH (CH-T) with delayed TSH elevation are included as screening targets. Data collected on CH-C patients using a regional survey, as well as data from a database created by a screening organization, were used. Of the 24 CH-C patients who had been born in Kanagawa Prefecture between 1999 and 2008, a positive screening result for FT4 (<0.7 ng/dL) was obtained in 13 newborns; of these, 12 were identified solely through newborn screening. Of the 113 patients for whom positive screening results were obtained during the study period, 5 and 6 were found to have transient CH-C and CH-T with delayed TSH elevation, respectively. Remarkably, 4 out of 5 patients with transient CH-C and all patients with CH-T with delayed TSH elevation were diagnosed through the evaluation of low FT4 at screening. These results indicate that the use of this FT4 screening system facilitates the identification of transient CH-C and CH-T with delayed TSH elevation, thus justifying the inclusion of these entities as screening targets.