Background Acute kidney injury (AKI) is one of the most common emergencies and severe diseases in the clinic. We sought toverify whether remote ischemic preconditioning (RIPC) has a protective effect on the kidney of child with congenital heartdisease undergoing cardiopulmonary bypass (CPB) surgery. We hypothesized it may be related to the up-regulation ofmicroRNA-21 (miR-21).Methods We performed a prospective randomized clinical study among children with congenital heart disease undergoing CPBsurgery between January and December 2016. Children were randomized to an RIPC or control group. Patients in each groupwere divided into an AKI and a non-AKI group according to the occurrence of AKI at 48 h after surgery. Remote ischemicpreconditioning (RIPC) conducted by blood-pressure cuff was performed 12 h before surgery. Serum creatinine (SCr), tumornecrosis factor-α (TNF-α), and miR-21 expression in blood and urine were measured at different time points.Results A total of 449 cases (200 RIPC; 249 controls) were enrolled. The male/female ratio was 1.18, with a mean age of 37.50 ±25.31 months. The incidence of AKI in the RIPC group was significantly lower than that in the control group (19.0% vs. 46.2%,P