ABSTRACT Adolescent elite-level footballers are exposed to unique physical and psychological stressors which may increase injury risk, with fluctuating injury prevalence and burden. This study investigates the patterns of injury incidence and burden from 2017 to 2020 within combined pre-, start-of-, mid- and end-of-season and school-holiday phases in U13-U18 Australian male academy players. Injury incidence rate and burden were calculated for medical attention (MA), full and partial time-loss (TL) and non-time-loss (non-TL) injuries. Injury rate ratios (IRR) for injury incidences were assessed using Generalised Linear Mixed Models, and 99% confidence intervals for injury burden differences between phases. MA and non-TL injury incidence rates were higher during pre-season (IRR 1.65, p = 0.01; IRR 2.08, p = 0.02, respectively), and mid-season showed a higher non-TL incidence rate (IRR 2.15, p = 0.02) and burden (69 days with injury/1000 hrs, CI 47–103) compared to end-of-season (25 days with injury/1000 hrs, CI 15–45). MA injury rates and partial TL injury burden were higher during school compared to holiday periods (IRR 0.6, p = 0.04; 61 partial days lost/1000 hrs, CI 35–104; 13 partial days lost/1000 hrs, CI 8–23). Season phase and return-to-school may increase injury risks for elite academy footballers, and considering these phases may assist in developing injury prevention systems.