Photobacteriosis, caused by Photobacterium damselae subsp. piscicida, is a major bacterial disease affecting cobia aquaculture, leading to high mortality rates and economic losses. This study evaluated the potential of Scutellaria baicalensis root extract as a natural antimicrobial and immunostimulant in cobia. A total of 540 cobia (average initial weight: 23.3–26 ± 2 grams) were assigned to six dietary with 0, 0.5, 1, 2, 3, and 5% of S. baicalensis root extract and fed for 12 weeks. Parameters measured included growth performance, survival rate, humoral immune responses (myeloperoxidase (MPO), peroxidase, and lysozyme activity), and cytokine-related gene expression (TLR-9, IL-1β, IgM, and TNF-α) in the spleen. Among the supplemented groups, the 1% and 2% doses showed the most significant improvement in immune and growth responses. The 0.5% dose produced moderate effects, while higher concentrations (3% and 5%) showed reduced or plateaued benefits, suggesting potential overstimulation or metabolic burden at higher doses. Additionally, 1% S. baicalensis exhibited enhanced immune responses, with increased MPO, lysozyme, and peroxidase activity in cobia. These findings demonstrate the efficacy of 1% S. baicalensis as a feed supplement for improving cobia health and immunity in aquaculture, offering a sustainable alternative to antibiotics.