Stroboscopic training has repeatedly been shown to improve visuomotor abilities. However, although performance improvements were attributed to visual processes, information on the neurophysiological mechanisms is missing. Part 2 of this study investigated the effects of stroboscopic training on neural visual and motor functions and its contribution to training-induced changes in visuomotor reaction time. Forty-five young elite badminton athletes participated in this study, of which 32 (age, 13.7 yr) were included in the final data analysis. Participants were assigned to an intervention (stroboscopic vision) or control group (normal vision). Before and after a 10-wk training and after a 6-wk retention period, participants performed visual perception and reaction tasks in response to visual motion stimuli. The N2 and N2-r motion onset visual-evoked potentials, its linear combination (Vlc), and the BA6 negativity potential were determined using a 64-channel EEG. A significant TIME-GROUP effect was observed for the Vlc score (P = 0.019, ηp2 = 0.18), indicating a lower Vlc in the intervention group. However, post hoc tests did not reach significance. Within-subject correlation analyses revealed that changes in reaction speed were related to latency changes in N2 (r = 0.59, P < 0.001), N2-r (r = -0.64, P < 0.001), and the combined Vlc (r = 0.68, P < 0.001). Regression analyses across participants including multiple (N2/N2-r) or single (Vlc) predictors provided an explained variance of >60% (N2/N2-r, r2 = 0.62; Vlc, r2 = 0.64). No training effects or correlations were observed for the BA6 negativity. The results indicate that faster visuomotor reactions after stroboscopic training are accompanied by accelerated visual perception and processing, whereas motor processes seemed to be unaffected. Stroboscopic training may be promising to specifically address the visual system in visuomotor-demanding sports.