Background Outcomes in well-resourced, intensive care units (ICUs) in Kenya are thought to be comparable to those in high-income countries (HICs) but risk-adjusted mortality data is unavailable. We undertook an evaluation of the Aga Khan University Hospital, Nairobi ICU to analyze patient clinical-demographic characteristics, compare the performance of Sequential Organ Failure Assessment (SOFA), delta-SOFA at 48 hours and Mortality Prediction Model-III (MPM-III) mortality prediction systems, and identify factors associated with increased risk of mortality. Methods A retrospective cohort study was conducted of adult patients admitted to the ICU between January 2015 and September 2017. SOFA and MPM-III scores were determined at admission and SOFA repeated at 48 hours. Results Approximately 33% of patients did not meet ICU admission criteria. Mortality among the population of critically ill patients in the ICU was 31.7%, most of whom were male (61.4%) with a median age of 53.4 years. High adjusted odds of mortality were found among critically ill patients with leukemia (aOR 6.32, p<0.01), tuberculosis (aOR 3.96, p<0.01), post-cardiac arrest (aOR 3.57, p<0.01), admissions from the step-down unit (aOR 3.13, p<0.001), acute kidney injury (aOR 2.97, p<0.001) and metastatic cancer (aOR 2.45, p = 0.04). The area under the receiver-operating characteristic (ROC) curve of admission SOFA was 0.77 (95% CI, 0.73–0.81), MPM-III 0.74 (95% CI, 0.69–0.79), delta-SOFA 0.69 (95% CI, 0.63–0.75) and 48-hour SOFA 0.83 (95% CI, 0.79–0.87). The difference between SOFA at 48 hours and admission SOFA, MPM-III and delta-SOFA was statistically significant (chi2 = 17.1, 24.2 and 26.5 respectively; p<0.001). Admission SOFA, MPM-III and 48-hour SOFA were well calibrated (p >0.05) while delta-SOFA was borderline (p = 0.05). Conclusion Mortality among the critically ill was higher than expected in this well-resourced ICU. 48-hour SOFA performed better than admission SOFA, MPM-III and delta-SOFA in our cohort. While a large proportion of patients did not meet admission criteria but were boarded in the ICU, critically ill patients stepped-up from the step-down unit were unlikely to survive. Patients admitted following a cardiac arrest, and those with advanced disease such as leukemia, stage-4 HIV and metastatic cancer, had particularly poor outcomes. Policies for fair allocation of beds, protocol-driven admission criteria and appropriate case selection could contribute to lowering the risk of mortality among the critically ill to a level on par with HICs.