Radiation therapy is highly effective for the management of pediatric malignant central nervous system (CNS) tumors including embryonal tumors. With the increment of long-term survivors from malignant CNS tumors, the radiation-related toxicities have become a major concern and we need to improve the treatment strategies to reduce the late complications without compromising the treatment outcomes. One of such strategies is to reduce the radiation dose to craniospinal axis or radiation volume and to avoid or defer radiation therapy until after the age of three. Another strategy is using particle beam therapy such as proton beams instead of photon beams. Proton beams have distinct physiologic advantages over photon beams and greater precision in radiation delivery to the tumor while preserving the surrounding healthy tissues. In this review, I provide the treatment principles of pediatric CNS embryonal tumors and the strategic improvements of radiation therapy to reduce treatment-related late toxicities, and finally introduce the increasing availability of proton beam therapy for pediatric CNS embryonal tumors compared with photon beam therapy.