Evidence suggests that moderate physical activity (PA) positively relates to creativity and emotional intelligence (EI) in adolescents. However, it is unknown whether cooperative PA (physical exercises in pairs or small groups to enhance motivation, self-efficacy, and pro-social behaviours), performed over less time but at higher intensity, could have similar effects within a school setting. The aim was to analyse the effect of cooperative high-intensity interval training (C-HIIT) on creativity and EI in adolescents aged 12-16 years, and whether improvement effects are different according to weekly PA level. A randomised controlled trial was conducted with a control group (CG, n = 94), which did static stretching, and an experimental group (EG, n = 90), which performed C-HIIT. Both groups performed the activity during 16 minutes at the beginning of physical education (PE) classes. Creativity was assessed with one factor, and EI through four factors (well-being, self-control, emotionality, and sociability). Age and body mass index (BMI) were used as confounders. Both were measured twice (baseline and after 12 weeks). The EG increased well-being and sociability factors after the C-HIIT programme (both p < 0.001). More specifically, inactive adolescents in the EG showed significant improvements in comparison to the CG in creativity, well-being, and sociability (p = 0.028, p < 0.001, and p < 0.003, respectively). However, we did not find changes among active adolescents. A programme of C-HIIT in PE is a novel strategy to improve creativity and EI, especially in physically inactive adolescents. Starting PE classes with 16 minutes of C-HIIT could be recommended, independently of other activities planned for the session.