Thyroid nodule ultrasound-based risk stratification systems (US-RSSs) have been successfully used in adults to predict the likelihood of malignancies. However, their applicability to the paediatric population is unclear, especially in children with a history of radiation exposure, who are at a higher cancer risk. We tested the efficacy of three US-RSSs in this setting by retrospectively applying three classification systems (ACR-TIRADS, ATA and EU-TIRADS) to all paediatric patients referred for thyroid nodules and with a radiation exposure history. We compared the results with a reference standard (pathology or 36-month follow-up); sensitivity, specificity, positive and negative predictive values (PPV and NPV) and accuracy were calculated. A total of 52 patients were included; fourteen of them (27%) had papillary thyroid cancer (PTC) at the final histology. No significant differences across the US-RSSs were detected; specificity (range 95–97%) and NPV (range 88–93%) were particularly elevated. However, ACR-TIRADS, ATA and EU-TIRADS did not indicate the need for a biopsy in six (42.8%), seven (50%) and eight (57%) cases of PTC; in five cases, this lack of indication was due to a small (<1 cm) nodule size. In conclusion, US-RSSs show a high NPV and specificity in paediatric patients, whereas the cytology indication could be improved by reconsidering the dimensional criterion.