A 17-year-old adolescent boy presented with atypical major depressive episode (MDE) without specific focal neurological signs for 6 months. He had a diagnosis of intra-cranial germinoma, and the atypical MDE symptoms subsided after the operation. However, he had a relapse of atypical MDE 7 months after the first surgery. His mood and binge eating symptoms subsided, but intractable body weight gain only partially improved after treatment. When encountering manifestations of depression with atypical features, especially with binge eating symptoms in male children and adolescents, with early onset age, no family history, and prolonged depressive episodes, clinicians should consider not only mood disorders including bipolar spectrum disorders but also organic brain lesions such as intracranial germinoma.