Objective Medical assistance in dying (MAiD) is the medical provision of substances to end a patient’s life at their voluntary request. While legal in several countries, the implementation of MAiD is met with ethical, legislative and clinical challenges, which are often overshadowed by moral discourse. Our aim was to conduct a scoping review to explore key barriers for the integration of MAiD into existing health systems. Methods We searched electronic databases (CINAHL, Embase, MEDLINE, and PsycINFO) and grey literature sources from 1990 to 2017. Studies discussing barriers and/or challenges to implementing MAiD from a health system’s perspective were included. Full-text papers were screened against inclusion/exclusion criteria for article selection. A thematic content analysis was conducted to summarize data into themes to highlight key implementation barriers. Results The final review included 35 articles (see online Appendix 1). Six categories of implementation challenges emerged: regulatory (n = 26), legal (n = 15), social (n = 9), logistical (n = 9), financial (n = 3) and compatibility with palliative care (n = 3). Within four of the six identified implementation barriers (regulatory, legal, social and logistical) were subthemes, which described barriers related to legalizing MAiD in more detail. Conclusion Despite multiple challenges related to its implementation, MAiD remains a requested end-of-life option, requiring careful examination to ensure adequate integration into existing health services. Comprehensive models of care incorporating multidisciplinary teams and regulatory oversight alongside improved clinician education may be effective to streamline MAiD services.