This study evaluates the effects of a zinc-amino acid complex on broiler's intestinal permeability and integrity challenged with Clostridium perfringens. A total of 180 Arbor Acres 1-day-old male broilers were assigned to 6 treatments in a completely randomized 2 × 3 factorial design. The experiment investigated the comparative effects of inorganic and organic zinc supplements, that is (ZnSO4 treatment: 80 mg zinc/kg from ZnSO4; iso-dose replacement group. (ISO) treatment:40 mg zinc/kg from ZnSO4 plus 40 mg zinc/kg from a zinc-amino acid complex; and organic treatment: 40 mg zinc/kg from a zinc-amino acid complex) on C. perfringens-challenged broilers. C. perfringens, on the one hand, compromised intestinal mucosal barrier function by increasing the intestinal permeability of fluorescein isothiocyanate-labeled dextran (P < 0.05) and plasma endotoxin level, on the other hand, decreased both the transepithelial electrical resistance and the relative expression of occludin levels in the ileum at day 21 (P < 0.05). However, zinc supplement alleviates C. perfringens-induced pathologic changes in the intestinal permeability. ISO treatment, in particular, enhanced the villus height-to-crypt depth ratio and transepithelial electrical resistance and also reduced plasma endotoxin levels. In addition, zinc supplement relatively enhanced the expression of occludin levels in the ileum compared with the C. perfringens-challenged group. ISO treatment had the highest relative expression of occludin levels in the ileum. Thereby, the results indicated that partial replacement of ZnSO4 with a zinc-amino acid complex in the broiler diet could promote intestinal mucosal barrier function during C. perfringens infection via increased expression of occludin in the ileum.