To identify cumulative 5-year healthcare costs and healthcare days in children with anorectal malformation (ARM) and to compare the cumulative 5-year healthcare costs and healthcare days in children with ARM with 3 control cohorts: healthy, premature, and congenital heart disease (CHD).

We performed a retrospective case–control study using the Truven MarketScan database of commercial claims encounters between 2008 and 2017. The ARM, CHD, and premature cohorts were identified using a targeted list of International Classification of Diseases 9th or 10th Revision diagnosis and Current Procedural Terminology codes. The healthy cohort included patients without ARM, preterm birth, or CHD.

We identified 664 children with ARM, 3356 children with heart disease, 63 190 children who were born preterm, and 2947 healthy patients. At 5 years, the total healthcare costs of children with ARM ($273K, 95% CI $168K-$378K) were similar to the premature cohort ($246K, 95% CI $237K-$255K) and lower than the CHD cohort ($466K, 95% CI $401K-$530K, P < .001). Total healthcare days were similar in children with ARM (158 days, 95% CI 117-198) and prematurity (141 days, 95% CI 137-144) but lower than CHD (223 days, 95% CI 197-250, P = .02). In ARM, outpatient care (126 days, 95% CI 93-159) represented the largest contribution to total healthcare days.

Children with ARM accumulate similar healthcare costs to children with prematurity and comparable healthcare days to children with CHD and prematurity in the first 5 years of life. Outpatient care represents the majority of healthcare days in children with ARM, identifying this as a target for quality improvement and demonstrating the long-term impact of this condition.