The growing role of aquaculture in global food security has underscored the need for advanced immunological insights to protect fish health and boost productivity. As aquaculture’s importance rises, understanding fish immunity is crucial for developing effective vaccination strategies. Fish possess a specialized immune system with unique mucosal structures that enable resilience in aquatic environments. This review examines critical advances in fish mucosal immunity, particularly focusing on mucosal vaccines that target infection at primary entry points, such as the gills, skin, and gastrointestinal tract. Mucosal vaccination has demonstrated a compelling capacity to stimulate localized and systemic immune responses, offering enhanced protection against waterborne pathogens. Additionally, this review addresses knowledge gaps from previous research on the global aquaculture vaccines market by offering a regional perspective on industry developments, recent trends, and innovative vaccine formulations. In doing so, it highlights the role of mucosal vaccines in overcoming the specific challenges of fish farming and supporting sustainable aquaculture. This synthesis of current methodologies, industry practices, and future directions contributes to a deeper understanding of fish immunology, ultimately informing strategies to achieve optimal disease management and bolster global aquaculture resilience.