Congenital diaphragmatic hernia (CDH) is a rare and severe disorder with a high mortality rate among infants. Unilateral renal agenesis (URA) is a relatively common congenital urinary malformation. Here, we present the case of a newborn infant with left CDH associated with ipsilateral renal agenesis. The male patient was born weighing 3.850 g through normal spontaneous vaginal delivery at 38 weeks and 6 days of gestational age at a maternity hospital. He was transferred to our neonatal intensive care unit due to respiratory distress with tachypnea, grunting and cyanosis after birth. A chest radiography indicated parts of the bowel in the thoracic cavity, consistent with CDH. Renal ultrasonography indicated no kidney structure on the left side and a 5.6 cm right kidney with normal echogenicity. Repair of the diaphragmatic hernia was performed three days after birth. Most of the colon, small bowel, stomach and spleen were located in the left pleural cavity, but the left kidney was not seen. Subsequent dimercaptosuccinic acid scintigraphy indicated non-visualized functional cortical uptake in the left kidney on day 13 after birth. Thus, we report the successful treatment of a patient with CDH accompanied by URA.