Heart rate variability biofeedback (HRV-BFB) has been shown as useful tool to manage stress in various populations. The present study was designed to investigate whether the biofeedback-based stress management tool consisting of rhythmic breathing, actively self-generated positive emotions and a portable biofeedback device induce changes in athletes\' HRV, EEG patterns, and self-reported anxiety and self-esteem. The study involved 41 healthy male athletes, aged 16-21 (mean 18.34 +/- 1.36) years. Participants were randomly divided into two groups: biofeedback and control. Athletes in the biofeedback group received HRV biofeedback training, athletes in the control group didn\'t receive any intervention. During the randomized controlled trial (days 0-21), the mean anxiety score declined significantly for the intervention group (change-4 p < 0.001) but not for the control group (p = 0.817). In addition, as compared to the control, athletes in biofeedback group showed substantial and statistically significant improvement in heart rate variability indices and changes in power spectra of both theta and alpha brain waves, and alpha asymmetry. These changes suggest better self-control in the central nervous system and better flexibility of the autonomic nervous system in the group that received biofeedback training. A HRV biofeedback-based stress management tool may be beneficial for stress reduction for young male athletes.