Diagnosis and classification of poorly differentiated tumors with primitive features of the central nervous system heavily relies on molecular and genetic findings of the tumors. Although RB1 gene mutation underlies the development of retinoblastoma and many other systemic cancers, RB1 gene mutation in a brain tumor is mainly limited to infiltrating gliomas. We describe what we believe to be a hitherto unreported case of sellar/suprasellar embryonal tumor with distinctive Flexner-Wintersteiner rosette formation, and somatic RB1 gene mutation in a 5-month-old infant. There were no molecular features associated with the embryonal tumor with multi-layered rosettes, and there were no histological or genetic features of a germ cell tumor. A follow up of 14 months duration showed good clinical response to VETOPEC regimen and no development of retinal disease. Our case shows an interesting association between RB1 mutation and Flexner-Wintersteiner rosettes in an embryonal tumor of the central nervous system and underscores the utility of large scale next generation sequencing in helping to identify the genetic aberrations that may help in clinical pathologic correlations of unusual or out-of-place histologic findings.