Ectopic hamartomatous thymoma (EHT) is an extremely rare benign neoplasm. It is usually found at the root of the neck (frequently on the left) and does not usually impact adjacent tissues in clinically significant ways. While EHT manifests distinct pathological features, the lesion is either asymptomatic or may show nonspecific clinical features. We report one case of EHT which was assumed to be of low malignant potential since it severely compressed the inlet of left internal jugular vein as seen by computed tomography scan. To the best of our knowledge, this clinical finding of EHT is very rare. After the diagnosis and treatment of this patient, we believe that EHT or suspected EHT should be treated less invasively.