Elite athletes demonstrate higher perceptual cognitive abilities compared to non-athletes and those capacities can be trained. A recent study showed that differences were observed between male and female athletes in their cognitive abilities whereby male athletes showed superior perceptual abilities compared to female athletes. The purpose of this study was to investigate whether there were gender differences in athletes’ perceptual cognitive learning using a 3D-MOT tracking task. The study was performed on 72 young people from 16 to 22 years of age; athlete males and females and non-athlete males and females were distributed in four distinct groups. Five sessions comprised of three thresholds were performed with each participant. Results indicated that all participants benefited from training and significantly increased their speed thresholds. Initial scores showed that male athletes achieved higher speed thresholds than any other groups. Furthermore, after 5 weeks, female athletes obtained higher speed thresholds in comparison to their non-athlete counterparts. In conclusion, engaging in sporting activity is associated with improved perceptual-cognitive abilities and learning. The results support the notion that competitive sport-related activity is beneficial for perceptual-cognitive functions and emphasizes the benefits of participating in sport-related activities for improved brain function with an even greater impact for females.