This study aimed to determine the causes of chronic kidney disease (CKD) in Iranian children. In this systematic review and meta-analysis study, international (PubMed, Web of Science, Scopus, and Google Scholar) and national (SID, Magiran) databases were searched for articles published through December 30, 2017. The quality of the studies was determined using the Hoy instrument. Out of 2,117 initial studies, 13 studies performed on a total of 3,596 children were included in the final stage of the study. Based on the results of the random effects method (95% CI), the main causes of chronic kidney disease in stages 1-4 (CKD) were CAKUT (37%) and glomerulonephritis (19.96%); in stage 5 (ESRD) they were CAKUT (40.82%) and urological disorders (27.44%). Considering the high prevalence of CAKUT, glomerulonephritis and urinary problems, the use of comprehensive approaches can be very effective in enhancing the knowledge of patients about the causes of kidney disease. The results obtained from the present study can assist policymakers in more accurately planning screenings of the causes of CKD in Iranian children.