Objectives: We investigated pediatric rare disease researchers’ experiences and perspectives with research collaborations involving industry partners. Methods: This mixed methods study included a cross-sectional survey of academic/hospital-based Canadian pediatric rare disease researchers which informed semi-structured interviews with a subsample of survey participants. We analyzed survey data descriptively and interview data thematically, integrating findings narratively. Results: Of 126 survey respondents, 59 (47%) reported research collaborations with industry; we interviewed 10 of these researchers. Important benefits to collaborations with industry reported by survey participants and interviewees included access to funding and resources, while disadvantages stemmed from perceptions that partners had different motivations. Interviewees provided advice for future researchers including careful selection of an industry partner, relationship building, clear expectations, and utilizing supportive institutional structures. Conclusion: Our findings provide insights into the experiences of pediatric rare disease researchers and offer suggestions on how to conduct successful collaborative research with industry.