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Background Children with sickle cell anemia are at risk for stroke. Ischemic stroke risk can be identified among children ages 2–16 years with sickle cell anemia using transcranial Doppler ultrasound. Despite strong recommendations for transcranial Doppler screening in guidelines released by the National Heart, Lung, and Blood Institute, implementation of transcranial Doppler screening in sickle cell anemia remains suboptimal. The purpose of this study was to identify barriers and facilitators to transcranial Doppler screening in a large national consortium to inform subsequent implementation interventions. Methods A qualitative descriptive approach was used to conduct 52 semi-structured interviews with a sample of patients with sickle cell anemia, their parents or primary caregivers, and healthcare providers dispersed across the United States. Interviews took place from September 2018 through March 2019. Directed content analysis was conducted with an adapted version of the Multilevel Ecological Model of Health as an initial coding framework, completed July 2019. Frequency analysis was conducted to determine predominant barrier and facilitator themes. Results Fourteen barrier themes and 12 facilitator themes emerged representing all levels of the ecological framework. Two barrier themes (Logistical Difficulties and Competing Life Demands and Gaps in Scheduling and Coordination), and 5 facilitator themes (Coordination, Scheduling and Reminders; Education and Information; Provider and Staff Investment and Assistance; Positive Patient Experience; and Convenient Location) were predominant. Conclusions Barriers and facilitators to transcranial Doppler screening in children with sickle cell anemia are complex and occur across multiple ecological levels. One barrier theme and 3 facilitator themes were found to be optimal to address in subsequent implementation interventions.