The present study aimed to investigate the effects of 12 weeks inulin supplementation (10 g/d) on clinical indices and biomarkers of inflammation, gut permeability, and oxidative stress in eighty women with migraine. Before and after the trial, we assessed the migraine index (MI), migraine headache index score (MHIS), headache diary results (HDR), high-sensitivity C-reactive protein (hs-CRP), zonulin, nitric oxide (NO), and oxidative stress factors. Inulin supplementation improved total antioxidant capacity (284.07 vs. 26.92, P=0.046), and reduced hs-CRP (−0.69 vs. 0.14), NO (−5.65 vs. 2.57) and oxidative stress index levels (−0.21 vs. 0.05) compared to placebo. Moreover, inulin supplementation resulted in a significant decrease in the score of MHIS, MI, and HDR (all P-values < 0.05). However, no significant change was observed in total oxidative status, and zonulin levels. This study showed that inulin supplementation can favorably improve clinical symptoms, inflammatory and oxidative stress biomarkers in women with migraine.