While aquaculture intensification increases productivity and profitability, it can lead to increased susceptibility of fish to disease outbreaks. As such, the production of aquafeeds with immunomodulatory properties is currently of significant interest to the aquaculture sector with a view of improving on-farm welfare. This study aimed to assess the effectiveness of the brown seaweed Sargassum linearifolium fortified with the probiotics Lactobacillus casei and Saccharomyces cerevisiae through submerged fermentation in improving growth, overall health and the ability to resist Vibrio harveyi infection in barramundi, Lates calcarifer. Two seaweed-based diets, probiotic-fortified S. linearifolium (referred to as PF-SL) and S. linearifolium without probiotic fortification (referred to as SL), were compared with a standard barramundi diet (control). Barramundi juveniles weighing 4.25 ± 0.09 g were fed the test diets three times daily to satiety for 56 days. The results demonstrated a significantly higher growth performance in fish fed the PF-SL diet when compared to the control. However, there were no notable differences in the apparent digestibility coefficient (ADC) of dry matter, protein, and lipid between PF-SL and control. Fish fed the PF-SL diet showed improved mucosal barrier function in both the skin and intestine, as indicated by the increased density of mucous cells. Similarly, fish fed the PF-SL diet exhibited higher glutathione peroxidase and total antioxidant activity than the control. The qRT-PCR revealed significant upregulation in the expression of anti-inflammatory genes (occludin, claudin1 and nrf2) and downregulation in the expression of proinflammatory genes (hsp70 and tnf-α) in fish fed the PF-SL diet. Furthermore, the PF-SL diet resulted in a 27% mortality in a 14-day challenge trial with V. harveyi, which was lower than the mortality rates of the SL (46%) and control (67%). Overall, this study demonstrates that feeding juvenile barramundi with probiotic-fortified brown seaweed S. linearifolium was able to improve growth, immunity, and resistance against Vibrio harveyi infection, suggesting significant potential for application across the aquaculture industry for improved fish welfare.