To investigate: (1) the injury epidemiology in an Australian academy; (2) how athletes transition through the high-performance sport (HPS) pathway; and (3) why athletes leave this HPS program. This retrospective cohort study was conducted at an Australian HPS academy over a 4-year period. Medical attention injuries were prospectively recorded. Injury incidence rates (IIR) and burden were calculated per 365 athlete-days, according to sport, sex, and pathway level. Athlete pathway levels were mapped to the Foundations, Talent, Elite, and Mastery (FTEM) framework. Reasons for athletes transitioning out were reported. Four hundred and eighty-one injuries were reported across 124 athletes at an IIR of 2.09 injuries per 365 athlete-days (95% CI = 1.91-2.29). Most athletes (103, 83.1%) were injured at least once over the 4-year period. IIRs increased (IRR = 1.17, 95% CI = 1.06-1.29, p = 0.001) as athletes progressed through the pathway. The most common reason for athlete attrition was deselection due to performance (n = 18), with 55.6% of these athletes sustaining an injury in the season prior to deselection. Injury burden was highest at E2 (119.5 days absence per 365 athlete-days (95% CI = 62.18-229.67)) and lowest at T4 (30.47 days absence per 365 athlete-days (95% CI = 21.98-42.24)). Injury occurrence is common across HPS, with IIRs increasing as athletes progressed to higher talent levels. Deselection due to poor performance was the main attrition factor, with more than half the deselected athletes impacted by injury prior to deselection. This study highlights an increased risk of deselection, following injury, and indicates the need for further development of prevention strategies targeting pathway athletes.