BackgroundComplementary and alternative medicine (CAM) is widespread but has various utilization rates according to country and the condition of patients. Generally, CAM is more frequently used in diseases that have no clear treatment method in conventional medicine. Therefore, a high utilization rate of CAM can be assumed in pediatric neurological diseases, but few studies have investigated the utilization of CAM in children with neuropsychiatric diseases. In particular, studies regarding the current use of CAM are scarce.MethodsWe conducted a survey of the parents or caregivers of patients who visited the pediatric rehabilitation clinic, pediatric neurology clinic, or pediatric psychiatry clinic at one university hospital from April to July 2011. We analyzed the factors that affect the utilization of CAM and other rehabilitation therapies.ResultsAmong the 578 patients recruited, 258 patients have ever received CAM (51.5 %), and the current CAM utilization rate was 19.0 % (110 patients). Two hundred patients (34.6 %) were currently receiving only other rehabilitation therapies, and 268 patients (46.4 %) were currently receiving no type of therapy. The rate of current CAM usage was significantly high in epilepsy patients.The ORs of 1–6-year-old and 7–12-year-old children compared with 13–19-year-old children were 3.14 (95 % CI 1.31–7.53) and 3.34 (95 % CI 1.64–6.79), respectively, and the OR of the group with longer disease duration (≥48 months) compared with the group with shorter disease duration was 3.36 (95 % CI 1.71–6.59). Only the age and disease duration showed statistically significant differences between the patients who were administered CAM and those who received other rehabilitation therapies (p < 0.0001).ConclusionsCAM is preferred by patients under 13 years of age compared with patients aged 13–19 years, whereas other rehabilitation therapies are preferred by patients aged 1–6 years, followed by those aged 6–12 years and then by those aged 13–19 years. The patient’s age and disease duration are the major factors influencing CAM use. Future studies should specify particular diseases, rather than combining all types of neuropsychiatric diseases, and include the socio-economic status of the parents.Electronic supplementary materialThe online version of this article (doi:10.1186/s12906-016-1066-4) contains supplementary material, which is available to authorized users.