This study examined injury and physical fitness outcomes in Basic Combat Training (BCT) during implementation of Physical Readiness Training (PRT). PRT is the U.S. Army's emerging physical fitness training program. An experimental group (EG, n = 1284), which implemented the PRT program, was compared to a control group (CG, n = 1296), which used a traditional BCT physical training program during the 9-week BCT cycle. Injury cases were obtained from recruit medical records and physical fitness was measured using the U.S. Army Physical Fitness Test (APFT, consisting of push-ups, sit-ups and a two-mile run). Injury rates were examined using Cox regression after controlled for initial group differences in demographics, fitness and other variables. Compared to the EG, the adjusted relative risk of a time-loss overuse injury in the CG was 1.5 (95 % confidence interval [CI] = 1.0 - 2.1, p < 0.01) for men and 1.4 (95 %CI = 1.1 - 1.8, p < 0.01) for women. There were no differences between groups for traumatic injuries. On the first administration of the final APFT, the EG had a greater proportion of recruits passing the test than the CG (men: 85 % vs. 81 %, p = 0.04; women: 80 % vs. 70 %, p < 0.01). After all APFT retakes, the EG had significantly fewer APFT failures than the CG among the women (1.6 % vs. 4.6 %, p < 0.01) but not the men (1.6 % vs. 2.8 %, p = 0.18); the gender-combined EG had a higher pass rate (1.6 % vs. 3.7 %, p < 0.01). Overall, the PRT program reduced overuse injuries and allowed a higher success rate on the APFT.