Arabinoxylan (AX) has been deemed as an antinutritional factor, but limited information has addressed the effects of dietary AX on intestinal health of fish. The present study investigated the effects of dietary AX on intestinal mucosal physical and immunological barriers of rainbow trout (Oncorhynchus mykiss). Five isoproteic and isolipidic experimental diets (AXE, AX0, AX2.5, AX5 and AX10) were formulated to contain 0.03% arabinoxylanase as well as 0%, 2.5%, 5% and 10% AX, respectively. Each diet was randomly distributed to triplicate groups of 35 juvenile (average weight 3.14 ± 0.02 g) per tank in a rearing system maintained at 17 ± 1 °C for 9 weeks. Dietary AX supplementation regardless of inclusion levels significantly (P < 0.05) depressed the growth performance and feed utilization. The plasma endothelin-1 and d-lactic acid contents as well as diamino oxidase activity were significantly higher in fish fed diet AX10 compared to fish fed diet AX0. Dietary inclusion of 5–10% AX resulted in decreased intestinal villus height, goblet cell number and desmosome density, increased crypt depth, short and irregular microvilli, widened intercellular space; down-regulated the mRNA levels of occludin in hindgut, claudin3 and ZO-1 in foregut and midgut, but up-regulated the mRNA levels of claudin12 and claudin15 in midgut as well as claudin23 in foregut, midgut and hindgut. Furthermore, dietary 5–10% AX supplementation decreased the midgut and hindgut complement 3, complement 4 and sIgT contents as well as the midgut IgM and hindgut IL-10 contents. Conversely, the hindgut TNF-α and IL-6 contents increased with the rising dietary AX level. RT-qPCR demonstrated that the pro-inflammatory cytokines (IL-1β, IL-6, IL-8, IL-12β, IFN-γ, and TNF-α) and pIgR mRNA levels in midgut and hindgut were up-regulated by dietary AX inclusion of 5–10% AX. Meanwhile, the mRNA levels of p38 MAPK, IκBα, and NF-κB p65 in midgut and hindgut raised gradually with the increasing dietary AX content. The Western blot results showed that the protein expression levels of p38 MAPK and NF-κB generally increased with the rising dietary AX content. Dietary treatment with 0.03% arabinoxylanase did not affect the growth performance and intestinal health of rainbow trout (P > 0.05). In conclusion, excessive dietary AX inclusion (5–10%) increased the intestinal permeability and induced the intestinal inflammatory response via activating MAPK/NF-κB signaling pathway, and ultimately damaged the intestinal barrier function of rainbow trout.