Aim The objective of this research was to determine the effectiveness of enzyme replacement therapy for juvenile-onset Pompe disease (patients aged 2 to 18 years at symptom onset) by systematic review. Methods A systematic search was conducted according to a protocol designed a priori of bibliographic databases and search engines. Studies selected according to pre-specified criteria were assessed for quality and risk of bias using standardised appraisal tools. Data were reported according to PRISMA conventions (Liberati et al. in PLoS Med 6:e1000100, 2009) and synthesised using GRADE (Guyatt et al. in J Clin Epidemiol 64:380-382, 2011). Results Of 2537 titles screened, 1 case series and 16 case reports met the inclusion criteria. No studies reported on the impact of enzyme replacement therapy on the survival of juvenile-onset patients. Low level evidence found that respiratory function may improve or be maintained in the early months of therapy. Improved muscle function in the first 6 to 12 months was also suggested, but results may be confounded by natural development. Patients with less severe baseline status and treated at a younger age showed more response than patients with more severe baseline status, treated as adults. Conclusions Interpretation of the findings was hindered by the lack of good quality evidence. The available data suggests that some JOPD patients may benefit in the short term from ERT through improved muscle strength and a reduced need for assisted ventilation. A focus by clinicians on improved and more consistent evidence collection, and use of study designs tailored to rare conditions, would provide more definitive results.