Following the Fukushima Daiichi Nuclear Power Plant (FNPP) accident on 11 March 2011, there have been concerns regarding the health impacts of the ensuing radioactive environmental contamination, which was spatially heterogeneous. This study aimed to assess the geographical variability of thyroid cancer prevalence among children and adolescents in Fukushima Prefecture. We computed the sex- and age-standardised prevalence ratio using 115 diagnosed or suspected thyroid cancer cases among approximately 300,000 examinees at the first-round ultrasound examination during 2011–2015 from 59 municipalities in the prefecture, under the Fukushima Health Management Survey. We applied flexibly shaped spatial scan statistics and the maximised excess events test on the dataset to detect locally anomalous high-prevalence regions. We also conducted Poisson regression with selected regional indicators. Furthermore, approximately 200 examinees showed positive ultrasound examination results but did not undergo confirmatory testing; thus, we employed simulation-based sensitivity tests to evaluate the possible effect of such undiagnosed cases in the statistical analysis. In conclusion, this study found no significant spatial anomalies/clusters or geographic trends of thyroid cancer prevalence among the ultrasound examinees, indicating that the thyroid cancer cases detected are unlikely to be attributable to regional factors, including radiation exposure resulting from the FNPP accident.