Salivary immunoglobulin A (IgA) plays a vital role in preventing upper respiratory tract infections (URTI). In our previous study, we showed that the intake of carbohydrates increases the intestinal levels of short-chain fatty acids (SCFAs), which in turn increase salivary IgA levels. However, the mechanism underlying this phenomenon has not been fully elucidated. In this study, we investigated in rats the effect of polydextrose (PDX) ingestion on salivary IgA level and SCFA concentration in cecal digesta and the portal vein. Five-week-old rats were fed with a fiber-free diet (control) or with 40 g/kg of PDX for 28 days. Compared to the control, ingestion of PDX led to a higher salivary IgA flow rate (p = 0.0013) and a higher concentration of SCFAs in the portal vein (p = 0.004). These two data were positively correlated (rs = 0.88, p = 0.0002, n = 12). In contrast, the concentration of SCFAs in cecal digesta and cecal digesta viscosity were significantly lower following PDX ingestion, compared to the control (p = 0.008 and 0.05, respectively). These findings suggest that the ingestion of PDX increases the absorption rate of SCFAs in the intestine through PDX-induced fermentation, which is accompanied by an increase in SCFA levels in the blood, and ultimately leads to increased salivary IgA levels.