Purpose Urethral carcinoma (UC), as a rare tumor, is not widely studied. There have been no systematic studies of rare pathological types of UC. We conducted this study to further investigate rare pathological types of primary urethral carcinoma (PUC). Materials and methods We used the population-based Surveillance, Epidemiology, and End Results (SEER) database to evaluate prognostic factors in rare pathological types of PUC. From 1978 to 2015, 2,651 and 257 cases were identified in the SEER database as common and rare pathological types of PUC, respectively. Overall and cancer-specific survival (CSS) times were computed using the Kaplan-Meier method, and the Cox proportional hazards analysis was used to evaluate patient age at diagnosis, gender, race, and TNM stage. Results The median overall survival (OS) rates were 36 and 59 months for rare and common pathological groups, respectively, and their respective 10-year OS rates were 31.9% and 42.4%, respectively. The median CSS rate was 61 months for the rare pathological group. Through multivariate analysis, it was found that age, race, T stage, and M stage were independent prognostic risk factors for rare pathological type of urethral cancer. In the age group, the HR ratio of patients aged older than 60 years and younger or equal to 60 years was 2.778 (P<0.001). The HR ratio of other races to Whites was 1.444 (P=0.040). In TNM staging, the HR ratio between T3-T4 and Ta-T2 was 2.386 (P=0.046), and the HR value of M1 and M0 was 5.847 (P<0.001). Conclusion Age, race, T stage, and M stage were predictive of OS and CSS in rare pathological PUC.