Food consumption is increasing due to rapid population growth. Fish is one of the most important animal foods, providing a high amount of energy in the form of proteins, essential amino acids, nutrients, vitamins, and minerals. Antibiotics are used to control several pathogens that harm fish. However, the use of antibiotics in fish causes numerous infections like tissue damage and immunological suppression. So, due to these side effects of antibiotics, probiotics and vaccines were introduced to protect fish from various pathogens. Probiotics are beneficial bacteria that have numerous positive effects on fish, while vaccines are precautionary measures that can prevent the fish from disease if administered to healthy fish. Several gram-positive and gram-negative bacteria are used as probiotics in fish, while different types of vaccines are used to control fish diseases, including both vibrioses as well as infectious hematopoietic necrosis. The dose, as well as the mode of administration of both probiotics and vaccines, are also significant factors that affect fish health. Vaccines and probiotics, if used in appropriate amounts, provide health benefits to fish. Although the effects of probiotics and vaccines may differ in different fish species, they are more useful than antibiotics. This review article discusses the beneficial effects of probiotics on fish as well as vaccines that are currently used to protect fish from disease.