We explored knowledge, beliefs, and acceptability of pre-exposure prophylaxis (PrEP) for HIV prevention with reference to stigma among people who inject drugs (PWID) in two predominately rural U.S. states. We conducted interviews with 65 current or former PWID aged 18 years or older and living in Arizona or Indiana. Most (63%) of the interviewees were not aware of PrEP. They often confused PrEP with HIV treatment, and many believed that PrEP was only for sexual risk or gay sexual risk. Once they understood that PrEP was recommended for PWID, the participants held a positive view of PrEP and felt that a once-daily pill was feasible. Experiences of stigma about drug use remained a crucial barrier to accessing healthcare and PrEP. This was often linked with anticipated or expressed homophobia. PrEP interventions among PWID must focus on education and the confluence of stigmas in which PWID find themselves when considering PrEP.