Background Deakin’s Rural Community Clinical School (RCCS) is a Longitudinal Integrated Clerkship (LIC) program in Western Victoria. Students undertake a year-long placement in a rural General Practice, many of which also host General Practice Registrars. There is a lack of evidence addressing the role and impact of Vertically Integrated Learning (VI) in practices hosting both LIC medical students and General Practice Registrars. The objective of the study was to establish how VI is perceived in the LIC context and the impact that it has on both learners and practices, in order to consider how to potentiate the role it can play in facilitating learning. Methods Semi-structured, in-depth, qualitative interviews were undertaken, with 15 participants located in RCCS General Practices. Emergent themes were identified by thematic analysis. Results Five main interconnected themes were identified; (i) understanding and structure, (ii) planning and evaluation, (iii) benefits, (iv) facilitators, and (v) barriers. Conclusion VI in a rural LIC is not clearly understood, even by participants. VI structure and methodology varied considerably between practices. Benefits included satisfying and efficient sharing of knowledge between learners at different levels. VI was facilitated by the supportive and collegiate environment identified as being present in a rural LIC context. Resources for VI are needed to guide content and expectations across the continuum of medical training and evaluate its role. The financial impact of VI in a rural LIC warrants further exploration.