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Objectives Youth football players are vulnerable to apophyseal injuries, which can have long-term consequences for health and performance. The objective was to assess the incidence, severity and burden of apophyseal injuries among U9–U21 academy football players over two seasons.Methods Time-loss injuries and match/training exposure were tracked in male academy football players (U9–U21) from Premier League and Category One Academies. Apophyseal injuries were identified in a cohort of 16 024 player-seasons using Orchard Sports Injury Classification System (OSICS) codes, and their incidence, severity and burden were analysed.Results A total of 10 589 injuries were reported, including 603 apophyseal injuries. These injuries followed a distal-to-proximal progression with age, occurring most frequently in the ankle/foot in younger players (U9, U10 and U11), followed by the knee (U12) and hip/groin in older players (U15, U16 and U18). Across all player phases (U9–U21), injury burden (days/1000 hours) was higher in the hip/groin (3.5) and knee (3.4), compared with the ankle/foot (2.2) and pelvis/sacrum (1.4), with the highest apophyseal incidence (~0.4 injuries/1000 hours) and burden (~20 days/1000 hours) observed in the U12–U16 group, regardless of injury location. A significant trend of increasing injury severity (median days) was observed with age: U9–U11 (20), U12–U14 (29), U15–U16 (38) and U18–U21 (35).Conclusions Apophyseal injuries exhibit a distal-to-proximal progression with age, with the highest injury burden observed at the hip/groin and knee regions and in the U12–U16 group. These findings can help inform injury mitigation strategies adopted in youth academy football.