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Many epidemics have afflicted humanity throughout history, claiming many lives. It has been noted in our time that heart disease is one of the deadliest diseases that humanity has confronted in the contemporary period. The proliferation of poor habits such as smoking, overeating, and lack of physical activity has contributed to the rise in heart disease. The killing feature of heart disease, which has earned it the moniker the “silent killer,” is that it frequently has no apparent signs in advance. As a result, research is required to develop a promising model for the early identification of heart disease using simple data and symptoms. The paper’s aim is to propose a deep stacking ensemble model to enhance the performance of the prediction of heart disease. The proposed ensemble model integrates two optimized and pre-trained hybrid deep learning models with the Support Vector Machine (SVM) as the meta-learner model. The first hybrid model is Convolutional Neural Network (CNN)-Long Short-Term Memory (LSTM) (CNN-LSTM), which integrates CNN and LSTM. The second hybrid model is CNN-GRU, which integrates CNN with a Gated Recurrent Unit (GRU). Recursive Feature Elimination (RFE) is also used for the feature selection optimization process. The proposed model has been optimized and tested using two different heart disease datasets. The proposed ensemble is compared with five machine learning models including Logistic Regression (LR), Random Forest (RF), K-Nearest Neighbors (K-NN), Decision Tree (DT), Naïve Bayes (NB), and hybrid models. In addition, optimization techniques are used to optimize ML, DL, and the proposed models. The results obtained by the proposed model achieved the highest performance using the full feature set.