Treatment of synchronous prostate and rectal cancers is a rare yet challenging problem with compounded toxicities. We report a case of a 65-year-old man who underwent proton beam therapy (PBT) with concurrent capecitabine and hormonal therapy for his synchronously found prostate (intermediate-risk) and rectal (cT2, N2b, stage IIIB) cancers; he also received low anterior resection. Before PBT, the patient experienced hematochezia. His baseline American Urological Association symptom score was a total of 0, and he was not sexually active. He completed PBT with grade 1 acute toxicities including fatigue, nausea, and increased urinary and bowel frequencies. He also developed mild anemia (10.7), which was resolved. Subsequent surgical pathology showed a pathologic complete response in his rectum. At follow-up of 2.5 years, he remained disease-free on surveillance imaging for both malignancies and reported increased bowel urgency and frequency, minimal urinary leakage when having urgency, and peripheral neuropathy. This case, along with a succinct literature review, demonstrates that PBT can be successful in the definitive treatment of synchronous prostate and rectal cancers with minimal toxicities. Further research is required to evaluate the efficacy and side effect profiles of PBT.