Several machine learning (ML) prediction models for neurodegenerative diseases (NDs) in type 2 diabetes mellitus (T2DM) have recently been developed. However, the predictive power of these models is limited by the lack of multiple risk factors. This study aimed to assess the validity and use of an ML model for predicting the 3-year incidence of ND in patients with T2DM. We used data from 2 independent cohorts-the discovery cohort (1 hospital; n=22,311) and the validation cohort (2 hospitals; n=2915)-to predict ND. The outcome of interest was the presence or absence of ND at 3 years. We selected different ML-based models with hyperparameter tuning in the discovery cohort and conducted an area under the receiver operating characteristic curve (AUROC) analysis in the validation cohort. The study dataset included 22,311 (discovery) and 2915 (validation) patients with T2DM recruited between 2008 and 2022. ND was observed in 133 (0.6%) and 15 patients (0.5%) in the discovery and validation cohorts, respectively. The AdaBoost model had a mean AUROC of 0.82 (95% CI 0.79-0.85) in the discovery dataset. When this result was applied to the validation dataset, the AdaBoost model exhibited the best performance among the models, with an AUROC of 0.83 (accuracy of 78.6%, sensitivity of 78.6%, specificity of 78.6%, and balanced accuracy of 78.6%). The most influential factors in the AdaBoost model were age and cardiovascular disease. This study shows the use and feasibility of ML for assessing the incidence of ND in patients with T2DM and suggests its potential for use in screening patients. Further international studies are required to validate these findings.