Litopenaeus vannamei, known as whiteleg shrimp, is susceptible to infection by pathogenic microorganisms such as viruses and bacteria. Therefore, the prevention of infections in this shrimp is important to regulate the outbreaks of pathogenic microorganisms. In this study, we investigated the effects of kefir as a functional feed additive on innate immunity, survival against WSSV (White Spot Syndrome Virus) and productivity of L. vannamei. As a result, the treatment of kefir could upregulate six of seven genes crucial for innate immunity of L. vannamei. Also, the treatment of kefir directly improved the survival rate of L. vannamei against WSSV infection. Finally, in order to determine whether kefir can improve the productivity of shrimp, we carried out field tests in three aquaculture farms in South Korea. The weight of shrimp fed kefir was increased by 120% as well as the length, compared with that of the control group. These results demonstrate that kefir can be utilized as a functional feed additive to improve both innate immunity and productivity of L. vannamei in shrimp farming with no use of antibiotics.