Purpose: To examine the effects of 24-h controlled carbohydrate intake on next day pre- and post-exercise inflammatory and hepcidin responses. Methods: In a crossover design, 12 well-trained endurance athletes (Ht 181.08 ± 7.68 cm; Wt 74.8 ± 11.5 kg, VO2peak 68.9 ± 7.2 ml kg−1 min−1) completed two experimental (2-day) trials. On day 1, participants completed a glycogen depletion task, including a 16-km run (80 % vVO2peak) and 5 × 1 min efforts (130 % vVO2peak) separated by 2-min recovery. Subsequently, strict dietary control was enforced for 24 h, where low carbohydrate (LCHO 3 g kg−1) or high carbohydrate (HCHO 10 g kg−1) diets were provided. Twenty-four hours later, participants completed an 8 × 3 min interval running session at 85 % vVO2peak followed by 3-h monitored recovery. Venous blood samples were collected pre-, immediately post- and 3-h post-exercise, which were analyzed for interleukin-6, serum iron, ferritin and hepcidin. Results: Interleukin-6 was elevated (p < 0.001) immediately post-exercise compared to baseline in both conditions, but was lower in HCHO (p = 0.015). Hepcidin levels were also lower at baseline (p = 0.049) in HCHO, and a large effect (d = 0.72) indicated a trend for lower levels at 3-h post-exercise compared to LCHO. Serum iron was increased post-exercise for both trials (p = 0.001), whereas serum ferritin remained unchanged. Conclusions: Twenty-four hours of controlled low carbohydrate intake resulted in higher baseline hepcidin levels and post-exercise IL-6 responses than a high carbohydrate intake. Such hormone increases may be induced by gluconeogenic signaling of the liver, and may negatively impact an athlete’s iron metabolism.