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Background The COVID-19 pandemic had a devastating impact on childhood routine immunization programs, resulting in increased measles mortalities and complications. In Zambia, the likelihood of measles-related deaths and complications in children was possibly increased because of high rates of unvaccinated children, late diagnosis, and poor case management, which could have been a consequence of exclusive focus on COVID-19 interventions. This study aimed at examining the effect of the COVID-19 pandemic on measles mortality and its predictors among patients seen at health facilities in Zambia. Methods We used longitudinal data (January 2020 to August 2023) from outbreak investigations and time series data from 2017 to 2023 to understand the impact of COVID-19 on measles immunization and know the predictors of measles mortalities. The period running from January 2017 to February 2020, just before the first reported COVID-19 case, was defined as pre-COVID-19, and March 2020 to December 2023 as post-COVID-19. Multivariable logistic regression analysis was used to determine predictors of mortality. A segmented Poisson regression model was used to determine the correlation between the underlying patterns of measles mortality and the commencement of the COVID-19 pandemic. Results A total of 3429 measles cases were reported during the study period. Of these, 1261 had complete metadata and were included in the analysis. The median age was 3 years (IQR, 1–7). Out of the 1261 enrolled, 54 (4.3%) were reported died. A total of 205 (21.0%) were IgM positive, and 207 (16.9%) were vaccinated. Monthly measles mortality increased by 220%, from 0.06 per 100,000 before COVID-19 to 0.23 during the pandemic. Predictors of mortality were younger age category (0–4) (AOR = 2.78; 95% CI 1.16–7.14), testing positive for measles IgM (AOR = 2.17; 95% CI 1.07–4.39), rush (AOR = 3.66; 95% CI 1.31, 6.21), and female sex (AOR = 1.90; 95% CI 1.04–3.50), which increased the odds of dying. However, being vaccinated (AOR = 0.06; 95% CI 0.01–0.42) reduced the odds of dying. Evidence for the COVID-19 effect was strongly associated with increased measles mortality (RR, 1.02; 95% CI 1.00, 1.04; 0.017) with a trend step change of 81% (RR, 1.81; 95% CI 1.14–2.87). There was also an increased trend of measles cases (RR, 1.04; 95% CI 1.01–1.06) during the pandemic. Measles dose 2 vaccination trends increased by about 0.3% during the COVID-19 pandemic due to the Supplementary Immunization Activity (SIA) (RR, 1.003; 95% CI 1.000–1.010). However, there was a dramatic drop of about 42% (RR = 0.58, 95% CI 0.46–0.72). Conclusions Measles caused a significant increase in child mortality during the pandemic period. A mix of systemic, clinical, and individual factors affected measles mortality. Prioritizing vaccine coverage, especially for younger children and marginalized populations; enhancing diagnostic and treatment capacities; and addressing gender and healthcare access disparities are all essential components of interventions aimed at lowering mortality. The findings suggest that public health interventions focusing on measles vaccination, rapid detection, and appropriate case management are crucial to reducing mortality and preventing further transmission. To achieve population immunity, sustained efforts are required to maintain high coverage rates.