Saccharomyces boulardii is a unique species of yeast previously characterized as a probiotic strain (CNCM I-745) among a few probiotic yeasts reported to date. Inulin is one of the most common prebiotics that exhibit twisted hydrocolloidal properties in dairy products. The present study was designed to develop a synbiotic yogurt by incorporation of S. boulardii and inulin at 1%, 1.5%, and 2% (w/v), comparing with the probiotic and control plain yogurts. Microrheological, microstructural, microbiological, sensory properties, and volatile compounds of the yogurt samples were evaluated. Microrheological analysis showed that addition of inulin to yogurt slightly reduced the values of G′ and G″, while solid–liquid balance (SLB) values confirmed more solid properties of the synbiotic yogurt (0.582~0.595) than the plain yogurt (0.503~0.518). A total of 18 volatile compounds were identified in the synbiotic yogurt, while only five and six compounds were identified in plain and probiotic yogurts, respectively. Physiochemical parameters such as pH, acidity, and protein content were in the normal range (as with the control), while fat content in the synbiotic yogurt decreased significantly. Addition of 1% inulin not only reduced syneresis but also maintained viability of S. boulardii after 28 days of storage. Microstructural and microrheological studies confirmed the dense, compressed, homogeneous structure of the synbiotic yogurt. Thus, addition of inulin improved the textural and sensory properties of the synbiotic yogurt, as well as survival of S. boulardii with viable count above 6.0 log CFU/g in yogurt, as generally required for probiotics. Therefore, novel synbiotic yogurt with desirable quality was developed as an effective carrier for delivery of the probiotic yeast exerting its beneficial health effects.