En bloc kidney transplantation (EBKT) is a technique used to transplant pediatric kidneys to adult recipients, but can lead to certain complications seldom found in single-kidney transplantation. We report a case of renal artery embolization after EBKT due to intractable unilateral hydronephrosis and highlight the technical details and challenges of the procedure. An 18-year-old female with MELAS syndrome underwent EBKT from a 10-month-old male baby. Two months later, the patient developed unilateral hydronephrosis and recurrent urinary tract infections, which was intractable to conventional therapy. Therefore, we underwent embolization of the problematic transplanted left kidney. Owing to the complicated anatomy and multiple angulations, multiple microcatheters, wires and support catheters were needed to select the renal arteries. Repeated procedures were required due to remnant flow from small branches and accessory renal arteries that were not easily visualized by conventional angiography, which were eventually detected by adjunctive use of 3-dimensional rotational angiography. Selective renal artery embolization after EBKT is challenging due to the short renal artery length and multiple angulations, yet it can still be performed safely and effectively by use of meticulous catheter-wire interactions and adjunctive intraoperative imaging techniques to delineate the precise anatomy of the target arteries. Selective renal artery embolization, which is less invasive than nephrectomy, can be considered if the culprit kidney must inevitably be sacrificed in en bloc kidney transplantation.