Background/aim The injury risk is high in adolescent elite athletes. However, little is known about how the injury risk changes when young talented athletes start studying at a sports high school. The primary aim was therefore to explore the risk of injury when the athlete starts to study at a sports high school. A secondary aim was to identify risk factors for injury. Methods A total of 489 athletes (age 15–16 years) were followed for 20 weeks, including 10 weeks before and 10 weeks after the athlete had started to study at a sports high school. Substantial injury was monitored in adolescent elite athletes using the Oslo Sports Trauma Research Centre Questionnaire. Results The results showed that the mean difference (md) in injury prevalence was significantly (p=0.001) higher across the 10 weeks after school had started (md 3.6; 95% CI 1.5 to 5.8), compared with the 10 weeks before. Female athletes had significantly (p<0.001) higher injury prevalence (md 6.4%; 95% CI 3.0 to 9.8) across the 10 weeks after school had started, whereas male athletes (md 0.9%; 95% CI -1.8 to 3.6) had not (p=0.530). Three significant (p<0.05) risk factors were identified; previous injury within the past 12 months (OR 3.23), higher training volume (OR 0.97) and lower well-being (OR 0.71). Conclusions Our results provide supporting evidence for increased injury risk in female adolescent elite athletes after the athletes had started to study at a sports high school.