Accurate temperature measurement with little or no discomfort that is safe, without risk of hospital-acquired infections or perforations, is the preferred choice of medical professionals in pediatric settings. The objective was to discover the preferable site for body temperature measurement using non-contact infra-red thermometer (NCIT) among pediatric patients. NCIT measurement at mid forehead (F), right temporal region (T), right side of neck- over-carotid artery area (N), jugular notch (J), sternum (S), umbilical region and sublingual region (U) were compared with digital axillary temperature (DAT) in a single attempt in 500 patients, aged between 2 to 5 years with fever. Data was analyzed using Pearson's correlation, paired T-test and Bland-Altman plot to assess the correlation and agreement between the DAT and NCIT sites. The mean temperature of NCIT-T (38.42 ± 0.64 °C) was more agreeable with DAT (38.42 ± 0.63 °C) compared to other body sites. The minimum mean bias of -0.00480 °C was noted for NCIT-F with 95% CI of -0.164-0.15; however, NCIT-F revealed many outliers as compared to NCIT-J. A strong positive correlation existed between DAT and NCIT sites (r value: 0.99-0.98). However, significant difference was found between DAT and NCIT-N, NCIT-F and NCIT-U (p value < 0.0001). NCIT-J is the most preferable choice for measuring body temperature and can be interchanged with DAT. It will help to deliver fast results with enhanced patient comfort due to its non-invasive nature.