Background: Evidence supporting physical activity (PA) as an effective modality in the prevention and management of non-communicable diseases is robust. Medical doctors are ideally placed to translate this into practice; however, realising this has proved challenging. To ensure doctors are well prepared, the training of medical students to be proficient in PA counselling seems essential. This study aimed to explore the PA counselling practice of junior doctors, to gain insight into how undergraduate training might influence their future practice. Methods: Interviews were conducted with 11 junior doctors recruited by purposive sampling from across seven different medical schools. All junior doctors were currently undertaking their post-graduate training in North-West England. Interviews were digitally recorded, transcribed verbatim and analysed using thematic analysis. Results: Themes developed from the data were PA attitudes and practices, and barriers and facilitators to PA counselling in clinical practice. Conclusion: The PA counselling practice of junior doctors was found to be inadequate, and attitudes towards PA promotion were particularly discouraging while in the hospital setting. Lack of training in PA counselling at both the undergraduate and postgraduate level and lack of support from consultants were major hindrances. However, unexplored opportunities exist for junior doctors to incorporate PA counselling into primary and secondary care and thus transform the practice of the next generation of doctors.