We examined the effects of a Pilates exercise program on the mucosal immune function in older women. The study population comprised 12 older women who were divided into a Pilates group (PG, n = 6) and a control group (CG, n = 6). Saliva samples were obtained from both groups before and after the experimental period for salivary secretory immunoglobulin A level measurement. In addition, acute high-intensity exercises were performed before and after the three-month Pilates exercise program. After three months, salivary flow was significantly higher in the PG than in the CG. After the acute high-intensity exercises were performed following the three-month Pilates exercise program, the salivary flow rate was significantly higher at all time points. The S-IgA secretion rate significantly increased 30 min after acute high-intensity exercise performed following the three-month Pilates exercise program. This study suggests that regular participation in a moderate-intensity Pilates exercise program can increase salivary flow rate and S-IgA secretion in older women.