Accurate temperature measurement is crucial for the perioperative management of pediatric patients, and non-invasive thermometry is necessary when invasive methods are infeasible. A prospective observational study was conducted on 57 patients undergoing elective surgery. Temperatures were measured using a dual-sensor heat-flux (DHF) thermometer (Tcore™) and a rectal temperature probe (TRec), and the agreement between the two measurements was assessed. The DHF measurements showed a bias of +0.413 °C compared with those of the TRec. The limits of agreement were broader than the pre-defined ±0.5 °C range (−0.741 °C and +1.567 °C). Although the DHF sensors tended to overestimate the core temperature compared to the rectal measurements, an error grid analysis demonstrated that 95.81% of the DHF measurements would not have led to a wrong clinical decision, e.g., warming or cooling when not necessary. In conclusion, the low number of measurements that would have led to incorrect decisions suggests that the DHF sensor can be considered an option for continuous temperature measurement when more invasive methods are infeasible.