Chronic kidney disease (CKD) is a significant concern for individuals with type 1 diabetes (T1D), impacting their quality of life and healthcare costs. Identifying T1D patients at greater risk of developing CKD is crucial for preventive measures. However, it is challenging due to the asymptomatic progression of CKD and limited nephrologist availability in many countries. This study explores machine learning algorithms to predict CKD risk in T1D patients using ten years of retrospective data from the Epidemiology of Diabetes Interventions and Complications clinical trial. Eleven machine learning algorithms were applied to twenty-two readily available features from T1D patients’ routine check-ups and self-assessments to develop 10-year CKD risk prediction models. In addition, we also proposed a heterogeneous ensemble model (STK) using a stacking generalization approach. The models’ performance was evaluated using different evaluation metrics and repeated stratified k-fold cross-validation. Several predictive models showed reliable performance in CKD risk prediction, with the proposed ensemble model being the best performing with an average accuracy of 0.97, specificity of 0.98, sensitivity/recall of 0.96, precision of 0.98, F1 score of 0.97, Kappa and MCC score of 0.94, AUROC of 0.99, and Precision-Recall curve of 0.99. The proposed machine learning approach could be applicable for CKD risk prediction in T1D patients to ensure the necessary precautions to overcome the risk.