Fe is an essential micronutrient required for optimal cognitive and physical performance. Cross-sectional studies indicate that training degrades Fe status in female military personnel; however, longitudinal studies to measure the direct impact of military training on Fe status and performance have not been conducted. As such, the objective of the present study was to determine the longitudinal effects of military training on Fe status in female soldiers. Fe status was assessed in ninety-four female soldiers immediately before and following a 9-week basic combat training (BCT) course. Fe status indicators included Hb, erythrocyte distribution width (RDW), serum ferritin, transferrin saturation and soluble transferrin receptor (sTfR). A 2-mile (3·2 km) run test was performed at the end of BCT to assess aerobic performance. Fe status was affected by BCT, as all Fe status indicators, excluding Hb, were diminished (P ≤ 0·01) at the end of BCT. Fe status indicators at the end of BCT (Hb and RDW) were associated (P ≤ 0·05) with running performance, as was the change in sTfR over the training period (r 0·320; P ≤ 0·05). In conclusion, Fe status in female soldiers is degraded during BCT, and degraded Fe status is associated with diminished aerobic performance. Female athletes and military personnel should strive to maintain Fe status to optimise physical performance.