Using functional feed ingredients to increase the intestinal health of Atlantic salmon (Salmo salar) could allow greater variation and higher inclusion of plant-based proteins in the feed. This is beneficial both for the fish feed industry and fish welfare. Components with strong bioactive properties, such as fucoidans from marine macroalgae, have a great potential as a functional feed ingredient. In the present trial, we challenged Atlantic salmon (Salmo salar) post-smolts with 17.8% soya HP48, a diet that has been shown to cause low-level intestinal inflammation. Fucoidan from Undaria pinnatifida was included at 0, 1, or 3% (Control, FUC1, and FUC3, respectively) to study its ability to alleviate this low-level inflammation . The fish were fed the diets in triplicate tanks for 59 days. At the end of the experiment, the fish were euthanised and the mid- and hind intestine were sampled for morphological-, integrity- (Ussing chamber) and gene expressional- (RNAseq) assessments. Addition of 3% fucoidan lowered the protein digestibility of the feed, however, this did not result in significant differences in the growth parameters. The paracellular permeability of the hydrophilic marker 14C-mannitol tended to decrease with the addition of fucoidan in both tissue segments. The active transport of l-lysine in the mid intestine was significantly reduced in a dose-dependent manner of fucoidan. An anti-inflammatory effect of fucoidan was observed in the hind intestine with significant reductions in the stratum granulosum width and lamina propria height of fish fed FUC1 and FUC3 compared to the Control. This suggests that U. pinnatifida fucoidan can have positive effect on both intestinal integrity and immune regulation of Atlantic salmon (Salmo salar).