This study investigated the effects of tuna hydrolysate (TH) inclusion in fishmeal (FM) based diets on the growth performance, innate immune response, intestinal health and resistance to Streptococcus iniae infection in juvenile barramundi, Lates calcarifer. Five isonitrogenous and isoenergetic experimental diets were prepared with TH, replacing FM at levels of 0% (control) 5%, 10%, 15% and 20%, and fed fish to apparent satiation three times daily for 8 weeks. The results showed that fish fed diets containing 5% and 10% TH had significantly higher final body weight and specific growth rate than the control. A significant reduction in blood glucose was found in fish fed 10%, 15% and 20% TH compared to those in the control whereas none of the other measured blood and serum indices were influenced by TH inclusion. Histological observation revealed a significant enhancement in goblet cell numbers in distal intestine of fish fed 5 to 10% TH in the diet. Moreover, fish fed 10% TH exhibited the highest resistance against Streptococcus iniae infection during a bacterial challenge trial. These findings therefore demonstrate that the replacement of 5 to 10% FM with TH improves growth, immune response, intestinal health and disease resistance in juvenile barramundi.