Varicocele is a common male disease defined as the pathological dilatation of the pampiniform plexus and scrotal veins with venous blood reflux. Varicocele usually impairs the scrotal thermoregulation via a hemodynamic alteration, thus inducing an increase in cutaneous temperature. The investigation of altered scrotal thermoregulation by means of thermal infrared imaging has been proved to be useful in the study of the functional thermal impairment. In this study, we use the Control System Theory to analyze the time-domain dynamics of the scrotal thermoregulation in response to a mild cold challenge. Four standard time-domain dynamic parameters of a prototype second order control system (Delay Time, Rise Time, closed poles locations, steady state error) and the static basal temperatures were directly estimated from thermal recovery curves. Thermal infrared imaging data from 31 healthy controls (HCS) and 95 varicocele patients were processed. True-positive predictions, by comparison with standard echo color Doppler findings, higher than 87% were achieved into the proper classification of the disease stage. The proposed approach could help to understand at which specific level the presence of the disease impacts the scrotal thermoregulation, which is also involved into normal spermatogenesis process.