Intraosseous myoepithelial tumors are very rare. Due to the low incidence and diverse histologic features, accurate diagnosis is challenging, necessitating ancillary immunohistochemistry. Moreover, genetic abnormality in this tumor was not revealed until recently. Although EWSR1 translocation is involved in half of the cases of intraosseous myoepithelioma, only a few cases have indicated its counterpart gene. We herein describe a case of intraosseous myoepithelioma with a novel localization in the fourth metatarsal bone of a 36-year-old female. Cytogenetic analysis using next generation sequencing detected a rare EWSR1-PBX3 fusion. Next generation sequencing could be useful in understanding the cytogenetic characteristics of intraosseous myoepithelioma, and in obtaining an accurate diagnosis of this rare condition.