Objective: To determine the effectiveness of physiotherapy plus conventional treatment (CT) compared to CT alone for the treatment of functional constipation (FC) in children aged 4-17 years in primary care. Methods: Pragmatic randomized controlled trial with 8 months follow-up. Primary care physicians recruited children diagnosed with FC (n=234), and pediatricians recruited newly referred children with a diagnosis of FC (n=11). CT comprised toilet training, nutritional advice, and laxative prescribing, whereas physiotherapy focused on resolving dyssynergic defecation. The primary outcome was treatment success over 8 months, defined as the absence of FC (Rome III criteria) without laxative use. Secondary outcomes included the absence of FC irrespective of continuation of laxative use and global perceived treatment effect. Results: Children were allocated to CT plus physiotherapy or CT alone (67 per group), mean (SD) age was 7.6 (3.5) years. Results of longitudinal analyses in the intention-to-treat population showed that the treatment success percentage was not statistically improved by adding physiotherapy to CT (aRR 0.80, 95%CI 0.44-1.30). At 4 months, fewer children receiving physiotherapy had treatment success (17%) than children receiving CT alone (28%), but this had equalized by 8 months (42% and 41%, respectively). The percentage of children without FC, irrespective of continuation of laxative use, was not statistically different between groups over 8 months (aRR 1.12, 95%CI 0.82-1.34). Notably, parents reported significantly more global symptom improvement after physiotherapy than after CT (aRR 1.40; 95%CI 1.00-1.73). Conclusions: We find no evidence to recommend physiotherapy for all children with FC in primary care.