Young athletes are constantly developing, and their performance reflects this ongoing process. By understanding performance variations and implementing appropriate training strategies, coaches and stakeholders can help young athletes develop their skills and athletic potential, as well as psychological well-being. Volleyball skills, such as explosive strength and serving precision, play a crucial role in determining the outcomes of volleyball matches. In contrast, mental well-being contributes to enhancing psychological performance. This prospective, randomized, parallel-group trial investigates the effectiveness of Pilates for young volleyball players. We investigated whether Pilates improves certain individual volleyball skills (explosive strength and serving precision) and certain psychological aspects (state of mindfulness) in young, male, 12–14-year-old athletes. Participation in this 12-week study involved 40 athletes (PG = 20; CG = 20). The Control Group had regular training and the Pilates Group had regular training plus twenty-four additional Pilates sessions. The Pilates Group showed a significant improvement in the variables under investigation by 4–7% (p < 0.001). Pilates training can improve individual volleyball skills in young male athletes and may also benefit overall psychophysical development. This study suggests that incorporating Pilates into training programs for young volleyball players can be beneficial for individual skill development and potentially overall psychophysical well-being, assuming an important role in the educational development of the young.