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Background Transition to adult care represents a vulnerable period for young people with special health care needs as they navigate multiple life transitions and developmental issues. Patient navigators are a promising intervention designed to facilitate the transfer from pediatric to adult care. However, consistent definitions, key tasks, roles and responsibilities are lacking in guiding the scope of practice and the implementation of patient navigators. Methods Fundamental qualitative description was utilized in this study to identify perceptions from health care providers about implementing a patient navigator service for young people with special health care needs in transition to adult care. A purposive sample of health care providers with a variety of backgrounds within pediatric and adult systems in Alberta, Canada were recruited. Semi-structured interviews with participants were analyzed using thematic analysis to inductively identify perceptions regarding the role of patient navigators. Results A total of 43 health care providers highlighted the need for a patient navigator service to encompass 4 key stages for young people with special health care needs transitioning from pediatric to adult services: (1) identification of young people with special health care needs and families requiring support, (2) preparation for transfer, (3) health system navigation and, (4) post-transfer support. Conclusions The results of this qualitative study provide guidance for the development of patient navigator interventions for young people with special health care needs, as well as provide support for current transition services offered across Canada. Electronic supplementary material The online version of this article (10.1186/s12913-019-4227-6) contains supplementary material, which is available to authorized users.