In medical science, imaging is the most effective diagnostic and therapeutic tool. Almost all modalities have transitioned to direct digital capture devices, which have emerged as a major future healthcare option. Three diseases such as Alzheimer's (AD), Haemorrhage (HD), and COVID‐19 have been used in this manuscript for binary classification purposes. Three datasets (AD, HD, and COVID‐19) were used in this research out of which the first two, that is, AD and HD belong to brain Magnetic Resonance Imaging (MRI) and the last one, that is, COVID‐19 belongs to Chest X‐Ray (CXR) All of the diseases listed above cannot be eliminated, but they can be slowed down with early detection and effective medical treatment. This paper proposes an intelligent method for classifying brain (MRI) and CXR images into normal and abnormal classes for the early detection of AD, HD, and COVID‐19 based on an ensemble deep neural network (DNN). In the proposed method, the convolutional neural network (CNN) is used for automatic feature extraction from images and long‐short term memory (LSTM) is used for final classification. Moreover, the Hill‐Climbing Algorithm (HCA) is implemented for finding the best possible value for hyper parameters of CNN and LSTM, such as the filter size of CNN and the number of units of LSTM while fixing the other parameters. The data‐set is pre‐processed (resized, cropped, and noise removed) before feeding the train images to the proposed models for accurate and fast learning. Forty‐five MR images of AD, Sixty MR images of HD, and 600 CXR images of COVID‐19 were used for testing the proposed model ‘CNN‐LSTM‐HCA’. The performance of the proposed model is evaluated using six types of statistical assessment metrics such as; Accuracy, Sensitivity, Specificity, F‐measure, ROC, and AUC. The proposed model compared with the other three types of hybrid models such as CNN‐LSTM‐PSO, CNN‐LSTM‐Jaya, and CNN‐LSTM‐GWO and also with state‐of‐art techniques. The overall accuracy of the proposed model received was 98.87%, 85.75%, and 99.1% for COVID‐19, Haemorrhage, and Alzheimer's data sets, respectively.