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Background The 2013–2016 West African Ebola epidemic has been the largest to date with >11 000 deaths in the affected countries. The data collected have provided more insight into the case fatality ratio (CFR) and how it varies with age and other characteristics. However, the accuracy and precision of the naive CFR remain limited because 44% of survival outcomes were unreported. Methods Using a boosted regression tree model, we imputed survival outcomes (ie, survival or death) when unreported, corrected for model imperfection to estimate the CFR without imputation, with imputation, and adjusted with imputation. The method allowed us to further identify and explore relevant clinical and demographic predictors of the CFR. Results The out-of-sample performance (95% confidence interval [CI]) of our model was good: sensitivity, 69.7% (52.5–75.6%); specificity, 69.8% (54.1–75.6%); percentage correctly classified, 69.9% (53.7–75.5%); and area under the receiver operating characteristic curve, 76.0% (56.8–82.1%). The adjusted CFR estimates (95% CI) for the 2013–2016 West African epidemic were 82.8% (45.6–85.6%) overall and 89.1% (40.8–91.6%), 65.6% (61.3–69.6%), and 79.2% (45.4–84.1%) for Sierra Leone, Guinea, and Liberia, respectively. We found that district, hospitalisation status, age, case classification, and quarter (date of case reporting aggregated at three-month intervals) explained 93.6% of the variance in the naive CFR. Conclusions The adjusted CFR estimates improved the naive CFR estimates obtained without imputation and were more representative. Used in conjunction with other resources, adjusted estimates will inform public health contingency planning for future Ebola epidemics, and help better allocate resources and evaluate the effectiveness of future inventions. [ABSTRACT FROM AUTHOR]