Our aim was to design a study to evaluate the effectiveness and cost-effectiveness of adding physiotherapy to conventional treatment for children with functional constipation in primary care. Physiotherapy is focusing on improving the coordination between the pelvic floor and abdominal musculature during bowel movement, while conventional treatment is mainly focusing on symptomatic relief of symptoms, therefore, we expect the effects of physiotherapy will be more sustainable than the effects of conventional treatment. In this paper we describe the final study design and how the design was adapted, to overcome recruitment problems.