Traffic accidents due to fatigue account for a large proportion of road fatalities. Based on simulated driving experiments with drivers recruited from college students, this paper investigates the use of heart rate variability (HRV) features to detect driver fatigue while considering sex differences. Sex-independent and sex-specific differences in HRV features between alert and fatigued states derived from 2 min electrocardiogram (ECG) signals were determined. Then, decision trees were used for driver fatigue detection using the HRV features of either all subjects or those of only males or females. Nineteen, eighteen, and thirteen HRV features were significantly different (Mann–Whitney U test, p < 0.01) between the two mental states for all subjects, males, and females, respectively. The fatigue detection models for all subjects, males, and females achieved classification accuracies of 86.3%, 94.8%, and 92.0%, respectively. In conclusion, sex differences in HRV features between drivers’ mental states were found according to both the statistical analysis and classification results. By considering sex differences, precise HRV feature-based driver fatigue detection systems can be developed. Moreover, in contrast to conventional methods using HRV features from 5 min ECG signals, our method uses HRV features from 2 min ECG signals, thus enabling more rapid driver fatigue detection.