Chronic kidney disease (CKD) constitutes a major health problem and one of the leading causes of death worldwide. Patients with CKD have impaired immune functions that predispose them to an increased risk of infections, as well as virus-associated cancers and a diminished vaccine response. In this study, we aimed to identify clinical and laboratory parameters associated with in-hospital mortality in patients evaluated in the department of emergency (ER) and admitted with the diagnosis of severe acute respiratory syndrome (SARS) caused by coronavirus disease 2019 (COVID-19) at the Baptist Hospital of Nicaragua (BHN). There were 37 patients with CKD, mean age 58.3 ± 14.1 years, admitted to BHN due to COVID-19, and among them, 24 (65.7%) were males (p = 0.016). During hospitalization, 23 patients with CKD (62.1%) died of complications associated with COVID-19 disease, which was a higher proportion (odds ratio (OR) 5.6, confidence interval (CI) 2.1–15.7, p = 0.001) compared to a group of 70 patients (64.8% males, mean age 57.5 ± 13.7 years) without CKD admitted during the same period in whom 28.5% died of COVID-19. In the entire cohort, the majority of patients presented with bilateral pneumonia, and the most common symptoms at admission were dyspnea, cough, and fever. Serum levels of D-dimer, ferritin and procalcitonin were significantly higher in patients with CKD compared with those without CKD. Multivariate analysis revealed that CKD, age (>60 years), and hypoxia measured in the ER were factors associated with increased in-hospital mortality. Among patients with CKD but not in those without CKD (OR 36.8, CI 1.5–88.3, p = 0.026), an increased monocytes-to-lymphocyte ratio (MLR) was associated with higher mortality and remained statistically significant after adjusting for confounders. The MLR measured in the ER may be useful for predicting in-hospital mortality in patients with CKD and COVID-19 and could contribute to early risk stratification in this group.