Primary clear cell tumors of the breast are uncommon and often present a diagnostic challenge. We describe an extremely rare case of glycogen-rich clear cell malignant myoepithelioma in a 43-year-old woman. Histologically, this tumor is composed of clear cells with abundant cytoplasmic glycogen particles. Immunohistochemically, these tumor cells show co-expression of vimentin, smooth muscle actin, epithelial membrane antigen, S-100 protein, and cytokeratin as evidence of myoepithelial cell tumor. The pathological staging of the patient is IIB (pT3N0M0) and the nuclear grading is 2. The patient demonstrated no evidence of recurrence or metastasis over a period of 42 months. We suggest that glycogen-rich clear cell malignant myoepithelioma be included in the histological differential diagnosis of clear cell tumors of the breast.