Orofacial clefts are congenital anomalies that cause substantial morbidity and mortality. This study aimed to investigate temporal and geographic trends in mortality among Brazilian individuals with orofacial clefts listed as the underlying cause of death on death certificates. A retrospective cross-sectional study was conducted using data from the Department of Informatics of the Brazilian Unified Health System (DATASUS) from 1996 to 2023. The mortality information system registered 987 deaths related to orofacial clefts, with 880 patients under 1 year of age. There was a downward trend in annual mortality rates from 1996 to 2019, followed by an increase from 2020 to 2023. The main associated cause of death was respiratory and cardiovascular disorders. The mortality rate for infants under 1 year with orofacial clefts showed greater variation than did the mortality rate of children who died of other causes. The reduction in mortality rates from 1996 to 2019 occurred during the expansion and strengthening of DATASUS and its coordination with other levels of healthcare. The rise in mortality between 2020 and 2023 coincided with a reduction in surgical procedures due to the COVID-19 pandemic. This study revealed a decline in deaths from orofacial clefts in Brazil over several decades. These findings emphasize the importance of addressing preventable causes of death, including respiratory infections and malnutrition. High mortality within the first year of life-particularly among newborns under 28 days-highlights a critical shortage of pediatricians and its impact on care for individuals with craniofacial anomalies.