Background: Probiotics and prebiotics are functional ingredients that provide health benefits to consumers but they are mainly incorporated in dairy products. Designing a non-dairy product in which probiotics and prebiotics would be incorporated would allow more consumers to benefit from their advantages. Objective: This study investigated the effect of supplementation of two different prebiotics, fructooligosaccharide (FOS) and inulin, on the viability of Bifidobacterium longum ATCC BAA-999 in coconut water. Methods: Two concentrations of prebiotics used were 1% and 2%. The physicochemical characteristics of fermented coconut water with B. longum for 9 h at 37oC and during refrigerated storage at 4oC for 2 weeks were analyzed. The viability of B. longum in fermented coconut water was maintained above the recommended therapeutic level (7 log CFU/mL) with or without supplementation with prebiotics. Results: Most distinct changes in colour (∆E > 3) occurred in fermented coconut water compared to unfermented coconut water. An increase in the total soluble solids was also observed in fermented coconut water with the increase in the concentration of prebiotics. There were no significant changes in the clarity, pH, and concentrations of shikimic and malic acids in the fermented coconut water with or without supplementation with prebiotics over the 2 weeks of storage. Acetic acid production was observed in the fermented coconut water with the highest acetic acid production in the fermented coconut water supplemented with 1% FOS after 2 weeks of storage. Conclusion: This study demonstrated the potential use of coconut water as a medium to produce a probiotic drink.