We conducted a scoping review of contextual factors impeding uptake and adherence to pre-exposure prophylaxis in transgender communities as an in-depth analysis of the transgender population within a previously published systematic review. Using a machine learning screening process, title and abstract screening, and full-text review, the initial systematic review identified 353 articles for analysis. These articles were peer-reviewed, implementation-related studies of PrEP in the U.S. published after 2000. Twenty-two articles were identified in this search as transgender related. An additional eleven articles were identified through citations of these twenty-two articles, resulting in thirty-three articles in the current analysis. These thirty-three articles were qualitatively coded in NVivo using adapted constructs from the Consolidated Framework for Implementation Research as individual codes. Codes were thematically assessed. We point to barriers of implementing PrEP, including lack of intentional dissemination efforts and patience assistance, structural factors, including sex work, racism, and access to gender affirming health care, and lack of provider training. Finally, over 60% of articles lumped cisgender men who have sex with men with trans women. Such articles included sub-samples of transgender individuals that were not representative. We point to areas of growth for the field in this regard.