The need to measure body temperature contactless and quickly during the COVID-19 pandemic emergency has led to the widespread use of infrared thermometers, thermal imaging cameras and thermal scanners as an alternative to the traditional contact clinical thermometers. However, limits and issues of noncontact temperature measurement devices are not well known and technical–scientific literature itself sometimes provides conflicting reference values on the body and skin temperature of healthy subjects. To limit the risk of contagion, national authorities have set the obligation to measure body temperature of workers at the entrance to the workplace. In this paper, the authors analyze noncontact body temperature measurement issues from both clinical and metrological points of view with the aim to (i) improve body temperature measurements accuracy; (ii) estimate the uncertainty of body temperature measurement on the field; (iii) propose a screening decision rule for the prevention of the spread of COVID-19. The approach adopted in this paper takes into account both the traditional instrumental uncertainty sources and clinical–medical ones related to the subjectivity of the measurand. A proper screening protocol for body temperature measurement considering the role of uncertainty is essential to correctly choose the threshold temperature value and measurement method to access critical places during COVID-19 pandemic emergency.