This study aimed to identify risk factors for training injuries resulting in referral to a remedial instructor (RI) or medical discharge (MD) among British Army recruits undertaking initial training. Physical performance and anthropometric data for 11,937 male and 1,480 female recruits were examined as potential risk factors for RI referral and MD, using Cox regression. There was a trend showing that female recruits' MD rates were higher than male recruits' rates (p = 0.096), and RI referral rates were significantly greater for women than for men (p = 0.041). The independent risk factors for MD were 2.4-km run time, ethnicity, and Army training regiment attended (p < 0.001), and those for RI referral were 2.4-km run time, ethnicity, Army training regiment attended, and body mass index (p < 0.001). Gender was not an independent risk factor for injury, suggesting that lower levels of aerobic fitness are the primary cause of the greater incidence of injury among female recruits during British Army initial training.