We report a case of ependymoma with unusual vacuolar features arising in the left occipital lobe of a 2-year-old child. The tumor was composed of cells with single or multiple cytoplasmic vacuoles and clear cells. Some cells showed a signet ring-like configuration. Clear cells were compactly arranged and showed an oligodendro-glioma-like appearance. In addition, there were cellular ependymoma-like areas including perivascular pseudorosettes. On immunohistochemistry, glial fibrillary acidic protein and vimentin were mainly detected in cytoplasmic processes, and epithelial membrane antigen (EMA) staining showed granular and small vesicular reactivity. Ultrastructural investigation demonstrated intercellular microrosettes with or without cilia and long zonula adherens-type junctions that are typical of ependymoma. Furthermore, many intracytoplasmic lumina (ICL) were observed. Some ICL had microvilli and some did not. The latter varied in size, and may have fused with each other to develop giant ICL which could correspond to the signet ring-like configuration. Small ICL without microvilli had an appearance similar to that of distended endoplasmic reticula. Serial semithin and ultrathin sections revealed that EMA-positive structures were consistent with ICL containing microvilli and intercellular microrosettes. To determine the presence of unusual vacuolated ependymoma, electron microscopical examination was required. However, light microscopy was useful for detecting EMA-positive microvesicular and granular structures.