The intrathoracic kidney is one of the rare causes of the congenital ectopic kidney. The present study discusses a case referred to our clinic with a pre-diagnosis of renal agenesis and a diagnosis of the intrathoracic ectopic kidney. The case is a 9-year-old patient who applied to our clinic complaining of abdominal pain. The left kidney could not be shown in the abdominal ultrasonography for the patient's abdominal pain. In the Tc-99m dimercaptosuccinic acid (DMSA) scintigraphy performed on this, the left kidney was detected far above its normal localization. On the thorax plus upper abdominal, the patient's computed tomography showed that the left kidney was intrathoracically located and the diaphragmatic hernia. The left kidney may not be visualized on ultrasonography in the patient. Therefore, the ectopic kidneys should be visualized by Tc-99m DMSA scintigraphy. In selected cases, computed tomography should be used to determine the proper localization of the intrathoracic kidney and whether there is a diaphragmatic hernia.