Identifying unique patients across multiple care facilities or services is a major challenge in providing continuous care and undertaking health research. Identifying and linking patients without compromising privacy and security is an emerging issue in the big data era. The large quantity and complexity of the patient data emphasize the need for effective linkage methods that are both scalable and accurate. In this study, we aim to develop and evaluate an ensemble classification method using the three most typically used supervised learning methods, namely support vector machines, logistic regression and standard feed-forward neural networks, to link records that belong to the same patient across multiple service locations. Our ensemble method is the combination of bagging and stacking. Each base learner’s critical hyperparameters were selected through grid search technique. Two synthetic datasets were used in this study namely FEBRL and ePBRN. ePBRN linkage dataset was based on linkage errors noticed in the Australian primary care setting. The overall linkage performance was determined by assessing the blocking performance and classification performance. Our ensemble method outperformed the base learners in all evaluation metrics on one dataset. More specifically, the precision, which is average of individual precision scores in case of base learners increased from 90.70% to 94.85% in FEBRL, and from 62.17% to 99.28% in ePBRN. Similarly, the F-score increased from 94.92% to 98.18% in FEBRL, and from 72.99% to 91.72% in ePBRN. Our experiments suggest that we can significantly improve the linkage performance of individual algorithms by employing ensemble strategies.