Background As pre-exposure prophylaxis (PrEP) scales up in sub-Saharan Africa, governments and implementers need to understand how to best manage national programs. Kenya’s national PrEP program offers an opportunity to review elements of program success within the health system and evaluate the utility of a national implementation framework. We explored health system considerations for PrEP implementation to understand how Kenya’s national PrEP implementation priorities align with those of PrEP service providers, peer educators, and program or county managers. Methods We conducted twelve key informant interviews (KII) and nine focus group discussions (FGDs) with PrEP program and county managers (n = 12), peer educators (n = 44), and PrEP service providers (n = 48). We recruited participants across a variety of cadres and experiences with PrEP programs. KIIs and FGDs focused on PrEP service delivery and program implementation. Data were collected by trained study staff, audio recorded, translated into English, and transcribed. We used framework analysis methods to systematically apply Kenya’s 2017 National PrEP Implementation Framework to the data and summarized findings according to the seven Implementation Framework domains. Results All respondents emphasized the important role of communication, coordination, training, and leadership in PrEP implementation. PrEP service providers and program and county managers highlighted the importance of efficient data collection and utilization, and improved resource allocation. Commodity security and research, while key elements of the PrEP Implementation Framework, were less commonly discussed, and research was less prioritized by respondents. Respondents highlighted the importance of coordinated PrEP service delivery across sites and programs to improve overall client experiences. Conclusion In the context of a nationally-scaled PrEP program, PrEP service providers, peer educators, and program and county managers value strong leadership, close coordination of services across sites, and expedient use of data to improve strategies and services. Kenya’s PrEP Implementation Framework aligns closely with the priorities of individuals involved in PrEP service delivery and management, and provides a comprehensive overview of health system considerations for effective implementation of a PrEP program at scale.