Primitive neuroectodermal tumors are derived from primitive neuroectodermal cells and belong to a highly malignant subgroup of round-cell tumors. Peripheral primitive neuroectodermal tumors of the penis are an extremely rare malignant form among penile neoplasms. These tumors are often difficult to diagnose due to atypical symptoms. Here, we report a case of a 24-year-old patient in China with a neoplasm localized at the base of his penis. The initial symptom was dysuria without any inducement. The results of blood and urine examinations indicated no abnormalities. The imaging examination results indicated a firm mass near the base of the penis. The hematoxylin and eosin (H&E) staining revealed round, small tumor cells with heterotypical darkened nuclei. In addition, immunohistochemistry (IHC) revealed strong and diffuse positive staining for CD99 (mic-2), VIM (vimentin), and NCAM1/CD56 (neural cell adhesion molecule 1). In addition, 60% of cells were positive for the cell proliferation marker Ki-67. Based on the above results, the case was diagnosed with peripheral primitive neuroectodermal tumor (pPENT). We reviewed the literature from 1999 to 2013 and identified reports of pPENT with a low incidence and atypical symptoms. Accurate diagnosis with multiple detection technologies, including laboratory diagnostic tests, imaging, morphologic and immunologic examinations, is very important to reduce the misdiagnosis rate.