Background For stroke prevention in patients with atrial fibrillation (AF), the decision-making around antithrombotic therapy has been complicated by older age, multiple comorbidities, polypharmacy and the different pharmacological properties of warfarin and the nonvitamin K antagonist oral anticoagulants (NOACs). The complexity of decision-making has been associated with a reluctance by health professionals to use antithrombotic therapy, leading to poor clinical outcomes. In order to improve stroke prevention in patients with AF, the contemporary perspectives of health professionals on the decision-making around antithrombotic therapy needs exploration. Objective To elicit emerging themes describing health professionals' perspectives on the decision-making around antithrombotic therapy for stroke prevention in patients with AF. Setting Sydney metropolitan area of New South Wales, Australia. Method A qualitative study based on face-to-face interviews was conducted from August to October 2014. Seven pharmacists, seven specialists, six general practitioners and six nurses practising in the Sydney metropolitan area and managing antithrombotic therapy for AF were interviewed until theme saturation was achieved in each subgroup. Interview transcripts were analysed using manual inductive coding. Main outcome measure Emerging themes describing health professionals' perspectives on the decision-making around antithrombotic therapy for stroke prevention in patients with AF. Results Three overarching themes emerged. (1) Comprehensive assessment is necessary for decision-making but is not always implemented. Health professionals mostly focused on stroke risk assessment, not on the bleeding risk and medication safety issues. (2) Health professionals from different disciplines have different preferences for antithrombotic therapies. Although the majority of health professionals considered warfarin as the first-line therapy, NOACs were preferred by neurologists and haematologists. (3) Health professionals focused on different aspects of the decision making process: GPs and specialists were concerned about the appropriate prescription of antithrombotics, while pharmacists and nurses focused on daily medication management by patients. Conclusion The decision-making process appears to be partially preference based rather than systematic, and health professionals from various disciplines focus on different parts of the decision-making process.