Background: Some pediatric tertiary care centres in North America supplement conventional care with complementary therapies, together known as pediatric integrative medicine (PIM). Evidence to support the safety and efficacy of PIM is emerging, but the cost-effectiveness of an inpatient PIM service has yet to be assessed. Methods/Design: This study is a pragmatic cluster controlled clinical trial. Usual care will be compared to usual care augmented with PIM in three pediatric divisions; oncology, general medicine, and cardiology at one large urban tertiary care Canadian Children's Hospital. The primary outcome of the feasibility study is enrolment; the primary outcome of the main study is cost-effectiveness. Other secondary outcomes include the prevalence and severity of key symptoms (i.e. pain, nausea/vomiting and anxiety), efficacy of PIM interventions, patient safety, and parent satisfaction. Discussion: This trial will be the first to evaluate the comparative effectiveness, both clinical and cost, of a PIM inpatient service. The evidence from this study will be useful to families, clinicians and decision makers, and will describe the clinical and economic value of PIM services for pediatric patients admitted to hospital.