The maldistribution of physicians, especially in rural areas, remains a global public health challenge. The internship programme for medical doctors is one of the efforts undertaken to address this issue. However, evidence aiming to disentangle this persistent challenge in the Indonesian context has been scant. This study aims to identify factors influencing medical doctors' intentions to practise in rural areas and how these factors affect their decisions. We adopted a sequential explanatory mixed-method design using a validated questionnaire. Then, focus group discussions were conducted with medical doctors from three different regions (West, Central, and East) to gain in-depth understanding of motivations, intentions, and barriers to practicing in rural areas. Participants were intern doctors who had been practising for at least 6 months in their internship locations. Quantitative analysis was based on a questionnaire addressing each factor, rated using five-point Likert scales, with bivariate and multivariate logistic regression analyses. The qualitative results were analysed using thematic analysis. In total, 498 respondents completed the questionnaire where 9.6%, 49%, and 40.9% intend to practise in rural, suburban, and urban areas, respectively. Three factors were positively associated with a preference for rural practice: prior living experience in rural areas, accessibility to cultural centres and events, and personal savings as funding resources during medical school. However, the importance of 'internet accessibility' was negatively associated with a preference for rural practice. Furthermore, the qualitative study involving 18 participants resulted in four main themes: the role of the internship programme in enhancing motivation as medical doctors, factors generally influencing the intention to practise, factors influencing the intention to practise in rural areas, and policy recommendations to increase the intention to practise in rural areas. Addressing the challenge of attracting and retaining medical doctors in rural areas requires multisectoral approaches involving both personal and professional factors. © 2024 The Author(s). Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.