Germ cell tumors usually occur in the gonads. Extragonadal germ cell tumors (EGCTs) are uncommon, and the head and neck region is a rare primary location. In this region, endodermal sinus tumors are relatively uncommon; they are typically recorded alongside teratomas and infrequently by themselves. When an endodermal sinus tumor arises in the neck, it can present with unique clinical and radiographic features and can be challenging to diagnose and manage. We report the peculiar case of a 25-year-old young adult who was suffering from a painful left-sided neck swelling for a year. Fine needle aspiration cytology (FNAC) of neck mass was performed and the cytomorphological features were suggestive of germ cell tumor. After the diagnosis, the patient received chemotherapy and was posted for wide local excision of the tumor. On microscopic examination, the tumor mass showed histopathological features suggestive of an endodermal sinus tumor.