Diagnostic delay remains a barrier to improving biliary atresia (BA) outcomes. We tested the implementation feasibility of a two stage BA newborn screening program in an integrated healthcare system. Methods: Under a waiver of consent, we measured direct bilirubin (DB) levels in well newborns undergoing standard of care hyperbilirubinemia screening at four hospitals. Initial DB was measured by modifying nursery admission electronic medical record order sets. Second‐stage DB was obtained at ~2 weeks of age under parental permission/informed consent (PP/IC). Implementation measures included the proportions of (1) eligible newborns that were screened before nursery discharge, (2) newborns undergoing second stage screening at ~2 weeks of age, and (3) newborns that underwent clinical evaluation for persistently elevated DB. Results: A total of 12,276 newborns met eligibility criteria for screening, of which 12,055 (98.2%) underwent first‐stage screening in the newborn nursery. Ninety‐four (0.78%) had elevated positive initial screens. Ninety newborns (95.7%) underwent second‐stage screening (n = 20) or contact was made with the primary care provider to recommend second‐stage screening (n = 70). Among all screened newborns, 15 (0.12%) had abnormal second screens. All had follow‐up clinical evaluation for potential cholestatic liver disease. No BA cases were identified through screening, though two infants who met exclusion criteria (admission to the newborn intensive care unit) were subsequently diagnosed with BA during the screening period. Conclusions: BA newborn screening is feasible in an integrated health network. Low consent rates have implications for future studies. Program infrastructure is required for implementation success and sustainability. What is Known: Diagnostic delay remains a barrier to improving biliary atresia (BA) outcomes.Newborn screening reduces diagnostic delay and may improve BA outcomes.Whether newborn screening can be implemented broadly is unknown. What is New: BA newborn screening is feasible in an integrated healthcare network and such a network may be an ideal setting to study effectiveness, cost‐effectiveness, and potential for harm.BA newborn screening requires infrastructure for success and sustainability.Low consent rates may impact the design of future studies.