Chronic functional constipation (CFC), defined as having one bowel motion every 3 to 15 days, occurs commonly in children. The frequency of CFC has been estimated to be as high as 36% of children who attend a consultation with a pediatrician. Sensitivity to cow’s milk protein has been proposed as a possible cause for CFC. For this study, 13 children diagnosed with CFC participated in this research. Nine participants who completed the soy arm all experienced resolution (p < 0.05) of their disease. These results suggest that soymilk was effective because the children were not allergic to it, unlike their allergy to cow’s milk.