ObjectivesWe aim to delineate the digestive congenital abnormalities burden in children under 14 years old between 1990 and 2021.DesignWe implemented data from the Global Burden of Disease (GBD) 2021 database to evaluate digestive congenital abnormalities burden with different measures in 204 countries and territories from 1990 to 2021. We present precise estimations with 95% uncertainty intervals. In addition, we computed the estimated annual percentage change (EAPC) to examine the temporal patterns of these indicators.SettingIt uses prevalence, deaths and disability-adjusted life years (DALYs) data from the GBD study to analyse this issue.ParticipantsPatients with digestive congenital abnormalities diagnosis.OutcomesTotal numbers, age-standardised rates (ASRs) of prevalence, mortality and DALYs and their EAPCs were the main outcomes among children aged 0–14 years.ResultsIn 2021, 2206.79 thousand prevalent cases were reported worldwide, with digestive congenital anomalies accounting for 47.16 thousand deaths and 4324.56 thousand DALYs among children aged 0–14 years. Digestive congenital anomalies prevalence was mitigated by 8.15% between 1990 and 2021, with the global ASR of prevalence declining to 40.09 per 100 000. Digestive congenital anomalies mortality was mitigated by 35.35% between 1990 and 2021, with an ASR of deaths declining to 0.77 per 100 000. The worldwide burden of digestive congenital anomalies decreased by 34.96% in terms of DALYs from 1990 to 2021, with an ASR of 70.44 DALYs per 100 000 population. There was a significant hindrance in the prevalence, particularly among older children. The likelihood of digestive congenital abnormalities peaked during infancy (2–4 years) in all regions.ConclusionWe highlight promising global declines in the digestive congenital anomalies burden among children over the past 32 years. Prevalence, deaths and DALYs associated with these anomalies have shown consistent decreases, although regional variations persist. These findings offer crucial insights for shaping effective prevention and management strategies for paediatric digestive congenital anomalies.