Pelvi-ureteric junction obstruction is one of the most common urological conditions found in children. Horseshoe kidneys are a predisposing factor and to find a vascular anomaly causing the obstruction is rare. A 2-year-old girl with two episodes of culture-positive febrile urinary tract infections (UTI), was found to have right sided hydronephrosis. Renal scan revealed decreased functioning of right kidney with scars. A contrast CT scan showed a horseshoe kidney with pelvi-ureteric junction obstruction on right side with dilatation of renal pelvis. During laparoscopic pyeloplasty, lower pole crossing vessels were detected, not reported on CT scan. A dismembered pyeloplasty with transposition of uretero-pelvic anastomosis anterior to lower pole vessels was done. Anomalous vasculature of kidney should be kept in mind during surgery in such cases. A dismembered pyeloplasty along with transposition of anastomosis is necessary to prevent recurrence.