Confectioneries contain high amounts of sugar. High consumption frequency of candies may lead to various health risks. Sugar in jelly candy can be substituted with fructo-oligosaccharides and xylitol as a healthy sugar. This study examined the effect of using fructo-oligosaccharides and xylitol as a sugar substitute on the pH, degree of Brix, water activity, moisture content, hardness, colour, syneresis, and sensory of jelly candy from pectin. Sucrose was substituted with fructo-oligosaccharides (5.47%, 10.93%, and 16.36%) and glucose syrup was substituted with xylitol (5.47%, 10.93%, and 16.36%). The results showed that substituting sugar with fructo-oligosaccharides and xylitol affected the jelly candy’s physical and chemical characteristics (p < 0.05). The higher the concentration of fructo-oligosaccharides and xylitol used, the lower the water activity, moisture content, and syneresis, as well as increasing the colour of the jelly candy compared to the control. Jelly candy with the highest sugar substitute concentrations obtained the softest of the jelly candy hardness. The sensory evaluation showed that panellists preferred jelly candy with sugar substitutions of 5.47% fructo-oligosaccharides and 5.47% xylitol.