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 counseling 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 two 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.