Including exercise alongside other therapeutic approaches may help to address dysfunctional exercise use and improve eating disorder treatment outcomes. However, traditional treatment teams often lack the expertise needed to safely prescribe exercise. The aims of this study were to explore the perceptions and experiences of Accredited Exercise Physiologists (AEPs) relating to working with clients diagnosed with eating disorders to identify the role they play in the treatment of eating disorders and identify future training needs. Individual semi-structured telephone interviews were conducted with 12 (n = 9 females) AEPs working in the eating disorders field. Thematic analysis was conducted to extract major themes from the interview transcripts. Five major themes were identified: (1) The role of AEPs in the treatment of individuals with eating disorders is comprehensive; (2) Treatment is more effective when all components are addressed; (3) The absence of therapeutic exercise within standard treatment protocols reflects limitations of traditional scope of practice and knowledge about the role of AEPs; (4) Methods of acquiring further knowledge are insufficient for those in current practice; and (5) Accredited comprehensive training is currently unavailable but needed. This qualitative study showed that AEPs believe they can play a major role in the treatment of eating disorders and that treatment outcomes for individuals are likely to be greatly enhanced when dysfunctional exercise is addressed. Multidisciplinary training is needed.