Screening for HIV and hepatitis C virus (HCV) are essential for identifying undiagnosed infections and linking individuals to care. We conducted a qualitative study to understand facilitators and barriers contributing to increased HIV and HCV infection screening and the linkage to care in Gilead's FOCUS HIV and HCV screening program in clinical settings. Individual in-depth interviews were conducted with nine clinical partners in FOCUS-supported sites and eight FOCUS regional leads who provided technical assistance to the sites. Content analysis was undertaken to identify key themes. Three themes emerged as facilitators: (a) "champions" to lead screening activities, (b) having support from clinic administrative leadership, and (c) coalescing staff support. Two themes emerged as barriers: (a) aligning institutional screening policies with local laws and (b) securing resources for screening implementation activities. Clinical settings implementing HIV or HCV infection screening programs may consider identifying a champion and consider legal and resource concerns to facilitate implementation of impactful programs.