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Under-five mortality (U5M) is considered a major public health issue directly impacts a country's development. This study analyzed the prognostic factors of U5M in Sri Lanka using data from the 2016 Demographic and Health Survey (DHS) of 8123 children. The study employed both a binary logistic regression model (BLRM) and a binary logistic random intercept multilevel model (BLRIMM) and compared the accuracy of each model's prediction percentage. The results showed that the BLRIMM had a higher correct prediction percentage (98.67%) compared to the BLRM (98.31%). The study found that children who were not breastfed (Odds Ratio (OR) = 116.74, 95% Confidence Interval (CI) = 62.97–216.41), were part of multiple births (OR = 3.73, 95% CI = 1.21–11.51), did not have a normal delivery (OR = 1.86, 95% CI = 1.11–3.12), were born to mothers who had experienced previous miscarriages or child loss (OR = 2.27, 95% CI = 1.26–4.11), and were born to mothers with a higher Body Mass Index (BMI) (OR = 1.05, 95% CI = 1.003–1.10) had higher odds of U5M. The odds of U5M were found to be lower among Buddhists (OR = 0.06, 95% CI = 0.01–0.50), Hindus (OR = 0.05, 95% CI = 0.01–0.46), and Roman Catholics (OR = 0.032, 95% CI = 0.003–0.307) compared to the "Other Religions" category in the dataset. The estimated covariance parameter of the random intercept (0.8231, p-value = 0.0405) indicated significant unobserved cluster-level variation in U5M. The study's results emphasize the importance of addressing religion related differences of U5M and improving maternal education regarding healthy lifestyle, proper food intake, the significance of breastfeeding, safe delivery methods, safety measures during pregnancy and childbirth in cases of multiple births, and proper child care after birth. [ABSTRACT FROM AUTHOR]