Purpose Iron-deficient athletes are often treated with long-term, low-dose iron therapy. Such treatments may be efficacious in correcting iron deficiency; however, the effect on acute and chronic iron metabolism and subsequent endurance capacity is less clear. Methods Fifteen national and international standard runners were identified as iron deficient nonanemic (IDNA) and assigned to either an intravenous iron treatment group or placebo group. Participants completed three exercise tests to volitional exhaustion, as follows: before treatment, within 24 h, and 4 wk after treatment. Results Serum ferritin, serum iron, and transferrin saturation were significantly improved in the iron group after intervention and compared with those in placebo (P < 0.05). Hepcidin levels were significantly greater before and after exercise after the iron injection (P < 0.05), and this was independent of changes in interleukin-6. There were no differences between groups in red cell indices, total hemoglobin mass, VO2max, submaximal blood lactate, running economy, RPE, or time to exhaustion (P > 0.05). Conclusions A single 500-mg intravenous iron injection is effective for improving iron status for at least 4 wk, but this does not lead to improved aerobic capacity. This investigation suggests that iron availability supersedes inflammation in the regulation of hepcidin in IDNA endurance athletes after acute intravascular iron injection treatment.