Proton beam therapy (PBT) is an advanced type of radiotherapy that shows a dosimetric advantage over photon beam therapy and provides superior dose distribution. PBT may improve patient survival by improving the local disease control while reducing toxicity to normal organs, which may result in fewer treatment-related complications. During the last decade, technological progress has opened up new possibilities in the planning and conducting of PBT, so indications have gradually expanded to different cancers. However, many biological aspects of PBT are still unclear, and its role in clinical settings is controversial. Proton therapy is considered to be safe and effective for different types of pediatric cancers, and suitable in treatment of ocular melanomas, chordomas, and chondrosarcomas. Future research and more prospective clinical studies with long-term follow-up are required in order to clearly determine the benefits and proper indications for PBT.