The aim was to analyse the effect of monitored cooperative high-intensity interval training (monitored C-HIIT) on memory, selective attention, concentration, mathematical calculation, and linguistic reasoning in adolescents. A randomized controlled trial was used with a control group (CG, n = 94), and an experimental group (EG, n = 90) that performed monitored C-HIIT at the beginning of physical education (PE) classes, during 12 weeks (24 sessions). The EG increased 14.2% in selective attention, 8.41% in concentration, and 15.5% in mathematical calculation relative to the CG after the monitored C-HIIT programme (all p < 0.001). These improvements are especially significant in inactive students (all p < 0.001), but there were no differences in memory or linguistic reasoning variables (p > 0.05). It is concluded that a 16-minute monitored C-HIIT programme applied at the beginning of PE classes improves some cognitive variables, especially in physically inactive adolescents.