Embryonal rhabdomyosarcoma (ERMS) is one of the commonest childhood tumors that usually presents as a small round cell tumor (SRCT). We report a case of an ERMS expressing frequent and prominent intranuclear cytoplasmic inclusions (INCIs). Our patient was a 3-year-old female child who presented with proptosis of the left eye with left sided cervical lymphadenopathy. Fine-needle aspiration (FNA) smears from both the orbital lesion and the cervical lymph nodes were cellular with features of a small round cell tumor (SRCT). The most striking cytologic feature observed was the presence of frequent and highly prominent INCIs. Despite the diagnostic dilemma caused by this unusual finding, a differential diagnosis of peripheral neurectodermal tumor (PNET) /Ewing's sarcoma, neuroblastoma, and ERMS was considered. Immunocytochemistry (ICC), using an appropriate panel of markers showed it to be a case of ERMS. Interestingly, though, not as frequent as on cytologic smears; INCIs could be appreciated even on biopsy material. INCIs in an ERMS are highly unusual and, to our knowledge, have not been documented so far. As a result of lack of any such cases in the literature, at present, the significance of this unique finding is not clear, and therefore needs to be investigated, as and when such cases are encountered in the future.