To comprehensively compare the survival outcomes of clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC), the study cohort included ccRCC and pRCC patients in 2004-2017 from the Surveillance, Epidemiology, and End Results (SEER) database, which comprises 18 registries. Primary outcomes including overall mortality (OM) and cancer-specific mortality (CSM) were evaluated. Subgroup analyses were conducted for different ages, race, and disease stages. A total of 112,270 cases were eligible for the current analysis, including 92,209 cases of ccRCC and 20,061 cases of pRCC. Univariate analyses suggested that pRCC has a more favorable outcome than ccRCC in terms of CSM (HR: 0.72, 95% CI: 0.68-0.75, p < 0.001) and OM (HR: 0.90, 95% CI: 0.88-0.93, p < 0.001). Multivariate-adjusted HRs suggested that pRCC has worse survival outcomes than ccRCC (adjusted HR: 1.08 for CSM and 1.05 for OM, both p < 0.05). Subgroup analyses showed that pRCC had a significantly poorer prognosis than ccRCC among patients ≤45 years old (HR : 1.59, 95% CI: 1.31-1.93, p < 0.001; HR : 1.63, 95% CI: 1.40-1.90, p < 0.001). Among patients with distant metastasis, those with pRCC had a higher risk of CSM and OM than those with ccRCC (HR : 1.28, 95% CI: 1.19-1.39, p < 0.001; HR : 1.30, 95% CI: 1.21-1.40, p < 0.001). Propensity score analyses for patients ≤45 years old and those with metastasis showed similar results. The lack of information on pRCC subtypes in the SEER database was a limitation. In conclusion, pRCC has poorer survival outcomes than ccRCC among patients younger than 45 years old and patients with distant metastasis.© 2020 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.