Physical activity questionnaires exist, but effective implementation in primary care remains an issue. We sought to develop a physical activity screen (PAS) for electronic medical record (EMR) integration by 1) identifying healthcare professionals' (HCPs), patients' and stakeholders' barriers to and preferences for physical activity counselling in primary care; and 2) using the information to co-create the PAS. We conducted semi-structured interviews with primary care HCPs, patients and stakeholders, and used content and thematic analyses to inform iterative co-design of the PAS. Interviews with 38 participants (mean age 41 years) resulted in 2 themes: 1) HCPs are willing to conduct physical activity screening, but acknowledge they don't do it well; and 2) HCPs have limited opportunity and capacity to discuss physical activity, and need a streamlined process for EMR that goes beyond quantifying physical activity. HCPs, patients and stakeholders co-designed a physical activity screen for integration into the EMR that can be tested for feasibility and effects on HCP behaviour and patients' physical activity levels. Novelty: EMR-integration of physical activity screening needs to go beyond just asking about physical activity minutes. Primary care professionals have variable knowledge and time, and need physical activity counselling prompts and resources. We co-developed a physical activity EMR tool with patients and primary care providers.