ObjectiveTo systematically assess the quality of evidence-based clinical guidelines on the treatment of children with juvenile idiopathic arthritis and to compare the differences and similarities between recommendations, so as to provide references for clinical application. MethodsDatabases such as the TRIP, PubMed, CNKI, VIP, WanFang Data, CBM, U.S National Guideline Clearinghouse and Guidelines International Network were searched to collect evidencebased guidelines on medication therapy for children with juvenile idiopathic arthritis. Methodological quality of included guidelines was assessed according to the AGREE Ⅲ instrument, and differences and similarities among recommendations were compared. ResultsTwo evidence-based clinical guidelines from Australia and China were included. Among 6 domains of the Australian guideline which were rated using AGREE Ⅲ instrument, "scope and purpose", "stakeholder involvement", "rigor of development", "clarity and presentation", "applicability" and "editorial independence" were scored more than 50%. As for Chinese guideline, "scope and purpose", "stakeholder involvement", "rigor of development", "clarity and presentation" and "editorial independence" was all scored more than 50%, but "applicability" was scored less than 50%. ConclusionThe included guidelines are of high quality and strongly recommended, but the recommendations might exist limitation for Chinese children. Thus, the development of relevant Chinese evidence-based guidelines are urgently needed.