Background: Some reported that positive surgical margin at radical prostatectomy (RP) was a prognostic factor of clinical recurrence and prostate cancer death, and others showed that was not necessarily true. The prostatic apex is most popular location of positive surgical margin at RP and the frequency of apex is reported to be about 20-40% of all positive cases. Prostatic apex is also reported to lack a well-defined capsule and to be hardly retracted during operation. In this study, we evaluated the effect of positive surgical margin at apex-only on prognosis after RP in a large cohort. Methods: We retrospectively evaluated 1019 patients with prostate cancer who underwent radical prostatectomy without neoadjuvant or adjuvant therapy at the hospitals that the authors were affiliated with between 2005 and 2013. The operative approach (open, laparoscopic, or robotic) was decided by each institution. All prostatectomy specimen slides were reviewed by a single genitourinary pathologist according to ISUP 2014 criteria. Recurrence following RP was defined according to AUA guidelines. Results: The median patient age was 67 (range, 45–80) years. The median initial PSA was 6.8 ng/ml (range, 0.4–82 ng/ml). The median follow-up period was 69 (range, 0.7–135) months. Pathological T stage was in 72.5% of pT2 (n = 739), 23.4% of pT3a (n = 238), and 4.1% of pT3b (n = 42). There were 163 Grade Group (GG) 1 cases, 502 GG 2, 217 GG 3, 39 GG 4, and 98 GG 5 cases. 372 cases had positive surgical margin. Details were 201 (54%) apex only, 57 (15%) anterior, 43 (12%) posterior, 76 (20%) lateral, 40 (11%) bladder. Some patients showed multiple positive surgical margin. The patients with positive surgical margin at apex-only showed significantly better prognosis than other locations (P = 0.0001). This result was confirmed in each operative approach (open; P = 0.008, laparoscopic; P = 0.001, robotic; P = 0.01). Conclusions: Among surgical margin positive patients after RP, those at prostatic apex-only showed lower biochemical recurrence than other locations regardless of operative approach. Physician should follow such a patient carefully without adjuvant therapy.