Background Sexually transmitted infections (STIs) disproportionately affect men who have sex with men. Although clinical practice guidelines recommend routine STI screening of men who have sex with men who have high-risk behaviors, extragenital STI testing rates have been low in HIV clinics across the nation. The University of Washington STD Prevention Training Center implemented an STI self-testing program at a large HIV primary care clinic in Seattle, WA, to facilitate extragenital STI testing. Methods We performed a mixed-methods program evaluation to assess health care provider acceptability of the program at 9 months after implementation. Twenty-eight clinicians were invited to complete an online survey. We conducted one-on-one, semistructured interviews with 6 clinicians and a focus group with 7 members of the clinic nursing staff. Survey responses were tallied. Conventional content analysis was performed on survey comments and transcripts from the interviews and focus group. Results Ninety-one percent of clinicians were either satisfied or very satisfied with the program. Perceived advantages of the program included saving time for clinicians, overcoming patient discomfort, and increasing patient access to testing. Perceived program disadvantages included unclear responsibility of directing patients through the self-testing process and incorrect sample collection and labeling. Conclusions Despite perceived disadvantages, the self-testing program was acceptable to clinicians and nursing staff, key population for successful program adoption. Implementation of STI self-testing programs in clinic settings could help to increase extragenital STI testing rates by removing provider and patient barriers to testing.