Pre-exposure prophylaxis (PrEP) is underused in the southern United States (US), a region with high HIV incidence. Clinical decision support (CDS) tools could increase PrEP prescriptions. We explored barriers to PrEP delivery and views of CDS tools to identify refinements for implementation strategies for PrEP prescribing and PrEP CDS tools. We conducted focus groups with health care providers from two federally qualified health centers in Alabama and analyzed the results using rapid qualitative methods. Barriers to PrEP included providers' lack of training in PrEP, competing priorities and time constraints during clinical visits, concerns about side effects, and intensive workload. We identified refinements to the planned implementation strategies to address the barriers, including training all clinic staff in PrEP and having CDS PrEP alerts in electronic health records sent to all staff. Development and deployment of CDS tools in collaboration with providers has potential to increase PrEP prescribing in high-priority jurisdictions.