Central nervous system (CNS) neoplasms are the second most common childhood malignancy after leukemia and the most common solid organ neoplasm in children. Diagnostic dilemmas with small specimens from CNS neoplasms are often the result of multifactorial etiologies such as frozen or fixation artifact, biopsy size, or lack of knowledge about rare or unfamiliar entities. Since the late 1950s, ultrastructural examination has been used in the diagnosis of CNS neoplasms, though it has largely been replaced by immunohistochemical and molecular cytogenetic studies. Nowadays, pathologic diagnosis of CNS neoplasms is achieved through intraoperative cytology, light microscopy, immunohistochemistry, and molecular cytogenetic results. However, the utility of electron microscopy (EM) in the final diagnosis of CNS neoplasms and investigation of its pathogenetic origin remains critical. Here, we reviewed the distinguishing ultrastructural features of pediatric CNS neoplasms and emphasize the continuing value of EM in the diagnosis of CNS neoplasms.