Yolk sac tumor (YST) is a rare malignant tumor originating from germ cells. YST normally originates from the gonads, rarely occurring in extragonadal sites. We report a 35-year-old man with YST arising in the omentum, which is the first reported case of a primary YST of the omentum in an adult male. The patient presented to the community hospital with abdominal distension. A CT scan showed thickening of the omentum with ascites. The patient underwent open biopsy of the omental mass. The Pathology Department of the hospital could not make a definitive diagnosis at that time, and the tumor was considered a cancer of unknown primary (CUP) origin with features of primary colorectal cancer based on the immunohistochemistry (IHC) findings of the biopsy specimen (CK7–/CK20+ and CDX-2+). He was then referred to our hospital. We found that serum α-fetoprotein was abnormally elevated to 7,144 ng/ml (normal <10.0), and reevaluation of the biopsy specimen revealed microcystic or reticular patterns of tumor cells with Schiller-Duval bodies typical of YST. The present case suggests that IHC is a very useful diagnostic tool for subtyping CUP but should be interpreted in the context of clinical and morphological findings.