HIV Pre-exposure Prophylaxis (PrEP) uptake among transgender (TG) people and gay men and other men who have sex with men (MSM) remains low, despite South Africa being the first African country to approve PrEP. This mixed-methods study used a two-phase explanatory sequential design: (1) quantitative analysis of cross-sectional surveys followed by (2) qualitative in-depth interviews. This study explored facilitators and barriers to PrEP uptake to identify strategies to increase utilization in these key populations. We conducted 202 cross-sectional surveys and 20 in-depth interviews between July 2021 and March 2022 in Soshanguve, Tshwane, Gauteng. Quantitative data were analyzed using univariate logistic regression; thematic analysis was performed for qualitative data. Findings show high willingness to use PrEP but low PrEP uptake. We outline strategies to facilitate PrEP use: (1) demystify daily PrEP by deploying community-engaged PrEP education campaigns; (2) capitalize on existing peer networks; and (3) expand accessible and culturally responsive PrEP service delivery models. We provide feasible recommendations to close the PrEP uptake gap in these key populations in South Africa.