Background The prognostic factors for COVID-19 in patients with chronic kidney disease (CKD) are uncertain. We conducted a study to compare clinical and prognostic features between hospitalized COVID-19 patients with and without CKD. Methods Fifty-six patients with stage 3-5 CKD and propensity score-matched fifty-six patients without CKD were included in the study. Patients were followed-up at least fifteen days or until death after COVID-19 diagnosis. The endpoints were death from all causes, development of acute kidney injury (AKI) or cytokine release syndrome or respiratory failure, or admission to the intensive care unit (ICU). Results All patients were reviewed retrospectively over a median follow-up of 44 days (IQR, 36-52) after diagnosis of COVID-19. Patients with CKD had higher intensive care unit admission and mortality rates than the patients without CKD, but these results did not reach statistical significance (16 vs. 19; p = 0.54 and 11 vs. 16, p = 0.269, respectively). The frequency of AKI development was significantly higher in predialysis patients with CKD compared to the other group (8 vs. 5; p < 0.001), but there was no significant difference between the groups in terms of cytokine release syndrome (13 vs. 8; p = 0.226), follow-up in the ICU (19 vs. 16; p = 0.541), and respiratory failure (25 vs. 22, p = 0.566). Multivariate logistic regression analysis revealed that respiratory failure and AKI were independent risk factors for mortality. Conclusion The mortality rates of COVID-19 patients with CKD had higher than COVID-19 patients without CKD. Also, AKI and respiratory failure were independently related to mortality.