Identification of people with elevated body temperature can reduce or dramatically slow down the spread of infectious diseases like COVID-19. We present a novel fever-screening system, F3S, that uses edge machine learning techniques to accurately measure core body temperatures of multiple individuals in a free-flow setting. F3S performs real-time sensor fusion of visual camera with thermal camera data streams to detect elevated body temperature, and it has several unique features: (a) visual and thermal streams represent very different modalities, and we dynamically associate semantically-equivalent regions across visual and thermal frames by using a new, dynamic alignment technique that analyzes content and context in real-time, (b) we track people through occlusions, identify the eye (inner canthus), forehead, face and head regions where possible, and provide an accurate temperature reading by using a prioritized refinement algorithm, and (c) we robustly detect elevated body temperature even in the presence of personal protective equipment like masks, or sunglasses or hats, all of which can be affected by hot weather and lead to spurious temperature readings. F3S has been deployed at over a dozen large commercial establishments, providing contact-less, free-flow, real-time fever screening for thousands of employees and customers in indoors and outdoor settings.