Columnaris disease (CD) caused by Flavobacterium columnare (F. columnare) is lack of knowledge on effective treatment measures. Bacterial pathogens require iron as an essential nutrient to infect the host. While hepcidin acts as a master regulator in iron metabolism, its contribution to host defense is emerging as complex and multifaceted. In vitro, recombinant Ctenopharyngodon idellus (C. idellus) hepcidin (CiHep) and synthetic CiHep both showed the ability to increase the expression of hepcidin and ferritin in C. idellus kidney cells, especially the recombinant CiHep. In vivo, recombinant CiHep improved the survival rate of C. idellus challenged with F. columnare. In addition, the fish fed diet containing recombinant CiHep (group H-1) had a higher survival rate than other pretreatment groups. The study showed that recombinant CiHep regulated iron metabolism causing iron redistribution, decreasing serum iron levels and increasing iron accumulation in the hepatopancreas. Moreover, the expression of iron-related genes was upregulated in various degrees at a different time except for group H-1. Immune-related genes were also evaluated, showing higher expression in the groups pretreated with CiHep at an early stage of infection. Of note, a clear upregulation of more immune genes occurred in the groups pretreated with recombinant CiHep than that pretreated with synthetic CiHep in the late stage of infection. In conclusion, the recombinant CiHep has a protective effect on the host response to bacterial pathogens. We speculate that hepcidin protects C. idellus against F. columnare infection via regulating the iron distribution and immune gene expression.