Perineuroma is a rare tumor originating from perineurium of the peripheral nerve. In contrast to neurofibroma and schwannoma, both of which arise from endoneurium and are immunohistochemically positive for S100 protein, perineuroma is negative for S100 protein; the fact makes the pathologic diagnosis difficult. As is well known, stem cells are highly associated with neuronal and organ developments in human embryos, and some neuronal cells are suspected to be derived from neuronal stem cells. Herein reported a very rare case of subcutaneous perineuroma negative for S100 protein but positive for a number of stem cell antigens; the case suggested that some perineuromas could arise from neuronal stem cells. A 68-year-old woman presented with a skin tumor of 10 mm in diameter in the foot. Physical examination revealed a small movable subcutaneous tumor, and resection was performed. Histologically, the tumor was a well-defined round tumor measuring 0.9 cm × 0.9 cm × 0.9 cm located in the subcutaneous tissue. No capsule was seen. The tumor was composed of hypocellular myxoid, neuroid tissues containing small areas of high cellularity where tumor cells resembled neuronal stem cells. Immunohistochemically, the tumor was negative for S100 protein, HMB-45, various cytokeratin (CK), EMA, α-SMA, desmin, p53, and many other antigens. The neuronal stem cell-like cells were positive for various stem cell antigens including NSE, KIT, bcl-2, chromogranin, synaptophysin, PDGFRA, MET, ErbB2, and CD34, as well as for vimentin and Ki-67 antigen (labeling index = 1.5%). Because the tumor was negative for S100 protein but positive for neuroendocrine molecules and neuronal stem cell antigens, the author diagnosed the tumor as perineuroma with stem cell features. Such a perineuroma has not been reported to date. The outcome of the patient was excellent.