Atrial fibrillation (AF) is the most common clinically significant cardiac arrhythmia and is an important risk factor for ischemic cerebrovascular events. This study used machine learning techniques to develop and validate a new risk prediction model for new-onset AF that incorporated the use electrocardiogram to diagnose AF, data from participants with a wide age range, and considered hypertension and measures of atrial stiffness. In Japan, Industrial Safety and Health Law requires employers to provide annual health check-ups to their employees. This study included 13 410 individuals who underwent health check-ups on at least four successive years between 2005 and 2015 (new-onset AF, n=110; non-AF, n=13 300). Data were entered into a risk prediction model using machine learning methods (eXtreme Gradient Boosting and Shapley Additive Explanation values). Data were randomly split into a training set (80%) used for model construction and development, and a test set (20%) used to test performance of the derived model. The area under the receiver operator characteristic curve for the model in the test set was 0.789. The best predictor of new-onset AF was age, followed by the cardio-ankle vascular index, estimated glomerular filtration rate, sex, body mass index, uric acid, γ-glutamyl transpeptidase level, triglycerides, systolic blood pressure at cardio-ankle vascular index measurement, and alanine aminotransferase level. This new model including arterial stiffness measure, developed with data from a general population using machine learning methods, could be used to identify at-risk individuals and potentially facilitation the prevention of future AF development.