Purpose: To evaluate the biochemical freedom from failure (bFFF) by risk group and treatment modality and the predictive factors of bFFF by risk group in patients with prostate cancer undergoing permanent seed implantation (PI) with or without external beam radiation therapy (EBRT) in a nationwide prospective cohort study in Japan (J-POPS) during the first 2 years. Methods and Materials: The analyses included 2,316 participants in 42 institutions. bFFF was evaluated using the Phoenix definition and calculated using the Kaplan-Meier method, with factors compared using the Cox proportional hazard model. Results: Median follow-up period was 60.0 months. The 5-year bFFF rates in all patients, 1,028 low-risk, 1,114 intermediate-risk, and 133 high-risk patients were 93.6%, 94.9%, 92.7%, and 91.1%. The 5-year bFFF rates in PI group and EBRT combination therapy group were 93.7% and 93.3%. On multivariate analysis, younger age, higher Gleason score (GS), higher percent positive biopsies (%PB), and lower prostate V100 (p=0.0012, 0.0030, 0.0026, and 0.0368) in all patients; younger age, higher pretreatment PSA, and lower prostate V100 (p=0.0002, 0.0048, and 0.0012) in low-risk; higher GS, higher %PB, and no hormonal treatment (HT) (p=0.0005, 0.0120, and 0.0022) in intermediate-risk; and higher GS and higher %PB (p=0.0329 and 0.0120) in high-risk patients were significantly associated with biochemical failure. Conclusions: PI with or without EBRT resulted in excellent short-term biochemical outcomes in all risk groups, especially in high-risk patients. Age, pretreatment PSA, and prostate V100 in low-risk; GS, %PB, and HT in intermediate-risk; GS and %PB in high-risk patients independently affected bFFF.