Background: Squamous cell carcinoma (SCC) of the rectum is a rare form of gastrointestinal malignancy. The current knowledge on the natural history is primarily derived from case series. Methods: Using the National Cancer Data Base (NCDB), we determined the prognostic factors and overall survival (OS) outcomes of rectal SCC reported to NCDB between 2004 and 2015. Kaplan-Meier method and log-rank test were used to perform OS analysis. Propensity matched analysis was undertaken to compare the OS outcomes between rectal and anal SCC. Results: Of the 3405 cases included in our analysis, 67% were female. Median age at diagnosis was 61 years and did not differ by sex. In stages I-III, patients who received definitive chemoradiation only (108 months) had a better median OS as compared to surgery alone (76 months) (p = 0.012). On multivariate analysis, age <60 years, female sex, and receipt of chemoradiation with or without surgery were independent predictors of better OS in stage I-III disease. Administration of chemoradiation was associated with better OS in stage IV disease. On propensity matched analysis comparing outcomes to anal SCC, OS of rectal SCC was inferior (79 months) to anal SCC (113 months) (p < 0.001), no such difference in OS was noted in the cohorts that received surgery plus post-surgical chemoradiation (p = 0.12). Conclusion: Outcomes of rectal SCC were dependent upon age, sex, comorbidity score, and therapy received. Chemoradiation alone or in combination with surgery was associated with a better median OS in patients with stages I-III.