Background <p>In recent years, our understanding of the various stress factors affecting the mental well-being of medical trainees during on-call work has grown. Although we have developed a general understanding, we still lack insight into the underlying interrelationships and causal effects of these factors, necessary to address and prioritize the mental health needs of young doctors.</p> Objectives <p>We aimed to measure the causal effects of selected stress factors related to on-call work contributing to occupational stress among General Practitioners (GPs) in training.</p> Methods <p>We identified key stress factors through a literature review and group discussion. Furthermore, we built a Directed Acyclic Graph (DAG) for each identified factor to draw valid causal inferences based on data collected from an observational survey.</p> Results <p>Our analysis indicated that GPs in training experience interruptions to leisure time, fear of potential work-related errors, and anticipatory and vigilant behaviour towards potential patient complaints as key contributors to elevated stress levels during on-call work.</p> Conclusion <p>Our study revealed the importance of psychological or emotional stressors during an on-call shift encountered by GPs in training, encouraging preventive measures.</p> Trial registration <p>Not applicable.</p>