Addressing fatigue is useful in a variety of scenarios and activities. Fatigue has recently been studied from a psychophysiological standpoint. As a result, the expression and impact of peripheral and central fatigue has been evaluated. Driving is one occupation where tiredness has disastrous consequences. BAlert is a smartphone app that approaches exhaustion with psychophysiological measures. More specifically, it evaluates the level of fatigue via heart rate variability (HRV) data and the cognitive compromise via Stroop effect. The goal of this study is to determine if there are gender differences in fatigue levels among professional drivers using the BAlert app. Statistically significant differences were found in the number of hours awake, in different parameters of HRV (AVNN, PNN50, RMSSD, and SDNN), in the level of stress, as well as in the cognitive response evaluated through the app. The results are discussed and their implications for the management of work fatigue are presented.