Generally, the injection method is recommended as the best efficient method for vaccine applications in fish. However, labor-intensive and difficult injection for certain fish sizes is always considered as a limitation to aquatic animals. To demonstrate the effectiveness of a novel oral delivery system for the piscine vaccine with nano-delivery made from nano clay, halloysite nanotubes (HNTs) and their modified forms were loaded with killed vaccines, and we determined the ability of the system in releasing vaccines in a mimic digestive system. The efficaciousness of the oral piscine vaccine nano-delivery system was evaluated for its level of antibody production and for the level of disease prevention in tilapia. Herein, unmodified HNTs (H) and modified HNTs [HNT-Chitosan (HC), HNT-APTES (HA) and HNT-APTES-Chitosan (HAC)] successfully harbored streptococcal bivalent vaccine with inactivated S. agalactiae, designated as HF, HAF, HCF and HACF. The releasing of the loading antigens in the mimic digestive tract demonstrated a diverse pattern of protein releasing depending on the types of HNTs. Remarkably, HCF could properly release loading antigens with relevance to the increasing pH buffer. The oral vaccines revealed the greatest elevation of specific antibodies to S. agalactiae serotype Ia in HCF orally administered fish and to some extent in serotype III. The efficacy of streptococcal disease protection was determined by continually feeding with HF-, HAF-, HCF- and HACF-coated feed pellets for 7 days in the 1st and 3rd week. HCF showed significant RPS (75.00 ± 10.83%) among the other tested groups. Interestingly, the HCF-treated group exhibited noticeable efficacy similar to the bivalent-vaccine-injected group (RPS 81.25 ± 0.00%). This novel nano-delivery system for the fish vaccine was successfully developed and exhibited appropriated immune stimulation and promised disease prevention through oral administration. This delivery system can greatly support animals’ immune stimulation, which conquers the limitation in vaccine applications in aquaculture systems. Moreover, this delivery system can be applied to carrying diverse types of biologics, including DNA, RNA and subunit protein vaccines.