A control group (CG, n = 1,138) that implemented a traditional Basic Combat Training (BCT) physical training (PT) program was compared to an evaluation group (EG, n = 829) that implemented a PT program newly designed for BCT. The Army Physical Fitness Test (APFT) was taken at various points in the PT program, and injuries were obtained from a medical surveillance system. After 9 weeks of training, the proportion failing the APFT was lower in the EG than in the CG (1.7 vs. 3.3%, p = 0.03). After adjustment for initial fitness levels, age, and body mass index, the relative risk of an injury in the CG was 1.6 (95% confidence interval [CI] =1.2-2.0) and 1.5 (95% CI = 1.2-1.8) times higher than in the EG for men and women, respectively. The newly designed PT program resulted in higher fitness test pass rates and lower injury rates compared to a traditional BCT physical training program.