Attentional resources are a cornerstone of both cognitive and academic performance. The purpose of this study was to analyse the effect of high-intensity interval training (HIIT) sessions on selective attention and visuoperceptual ability in young students. A total of 134 students (12.83 ± 1.23 years) joined this study. They were randomly assigned to a control group (CG) (n = 67), which watched a documentary, or an experimental group (EG) (n = 67), which performed 16 min of HIIT. Attention and visuoperceptual ability were assessed through the Perception of Similarities and Differences test (Caras-R test). A repeated-measures two-way ANOVA analysis was conducted. The CG showed an increased number of errors compared to the EG (p < 0.001) and showed a lower Impulsivity Control Index (p < 0.001) after the investigation. The EG, meanwhile, showed an increased number of hits (p < 0.001), Impulsivity Control Index (p < 0.001), and attentional efficacy (p < 0.001). In addition, the EG showed a decreased number of errors (p < 0.001) and omissions (p < 0.01). In conclusion, 16 min of HIIT was time-effective in improving selective attention and visuoperceptual ability in young students. These results show the importance of physical exercise and the promotion of physical activity breaks during the academic day to improve learning processes.