Medical graduates’ early career is known to be disorienting, and career decision-making is influenced by a complex set of factors. There is a strong association between rural background and rural undergraduate training and rural practice, and personal and family factors have been shown to influence workplace location, but the interaction between interest, training availability, and other work-relevant factors has not yet been fully explored. A qualitative study conducted by the Rural Clinical School of Western Australia (RCSWA) and WA Country Health Service (WACHS) explored factors influencing the decision to pursue rural work among junior doctors. Data collection and analysis was iterative. In total, 21 junior doctors were recruited to participate in semi-structured telephone interviews. Two main themes relating to the systems of influence on career decision-making emerged: (1) The importance of place and people, and (2) the broader context. We found that career decision-making among junior doctors is influenced by a complex web of factors operating at different levels. As Australia faces the challenge of developing a sustainable rural health workforce, developing innovative, flexible strategies that are responsive to the individual aspirations of its workforce whilst still meeting its healthcare service delivery needs will provide a way forward.