Aim Studies on the anticancer effects of synbiotic fermented soymilk are rare. The aim of the present study was to evaluate the effect of synbiotic fermented soymilk supplemented with xylooligosaccharides and inoculated with Weissella cibaria FB069 (FSMXW) in the proliferation of colon cancer cell and compare it with the effect of soymilk inoculated with Lactobacillus rhamnosus GG (LGG). Methods and Results Both FB069 and LGG were able to grow in soy-based products and rapidly reduce their pH as a result of fermentation. The addition of XOS significantly enhanced the acidification rate, viscosity and total cell concentration in fermented soymilk inoculated with W. cibaria FB069. However, the same effect was not observed following inoculation with LGG. Moreover, the synbiotic FSMXW showed higher dextran, folate, GABA and aglycone content. FSMXW inhibited the proliferation of Caco-2 and HCT116 cell lines, by reducing the transcription of MD2, TLR4, MyD88, and NF-kappa b. Conclusions The synbiotic soymilk containing XOS and W. cibaria FB069 increase nutrient and functional compounds through fermentation process. Significance and Impact of the Study Our finding suggests that W. cibaria and XOS can be potentially employed in developing functional foods and health-related products.