INTRODUCTION: To compare long term glomerular filtration rate (GFR) outcomes of partial nephrectomy and radiofrequency ablation performed for renal malignancy. MATERIALS AND METHODS: Renal function of 347 patients undergoing radiofrequency ablation (n = 142) or partial nephrectomy (n = 205) for renal malignancy between 1994 and 2011 were compared from a retrospective database at a single tertiary care center. Minimum 1 year of follow up was required, resulting in a mean follow up of 48.2 (SD +/- 28.2) months. Renal function was estimated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. The primary study outcome was progression of Chronic Kidney Disease (CKD) stage, calculated using the Kaplan-Meier life table method. Multivariate analysis was also conducted to determine the level of association between GFR decline and treatment modality. RESULTS: The 5 year freedom from CKD stage progression for radiofrequency ablation and partial nephrectomy was 85.4% (95% CI 76.8%-91.1%) versus 82.1% (95% CI 73.7%-88.1%) (p = 0.06). A longer follow up interval was associated with greater GFR decline, although hypertension, diabetes, age, and tumor size were not. CONCLUSION: Radiofrequency ablation provides similar long term renal function preservation benefit as partial nephrectomy.