Medical data classification is the process of transforming descriptions of medical diagnoses and procedures into universal medical code numbers. The diagnoses and procedures are usually taken from a variety of sources within the healthcare record, such as the transcription of the physician’s notes, laboratory results, radiologic results and other sources. However, there exist many frequency distribution problems in these domains. Hence, this paper intends to develop an advanced and precise medical data classification approach for diabetes and breast cancer dataset. With the knowledge of the features and challenges persisting with the state-of-the-art classification methods, deep learning-based medical data classification methodology is proposed here. It is well known that deep learning networks learn directly from the data. In this paper, the medical data is dimensionally reduced using Principle Component Analysis (PCA). The dimensionally reduced data are transformed by multiplying by a weighting factor, which is optimized using Whale Optimization Algorithm (WOA), to obtain the maximum distance between the features. As a result, the data are transformed into a label-distinguishable plane under which the Deep Belief Network (DBN) is adopted to perform the deep learning process, and the data classification is performed. Further, the proposed WOA-based DBN (WOADBN) method is compared with the Neural Network (NN), DBN, Generic Algorithm-based NN (GANN), GADBN, Particle Swarm Optimization (PSONN), PSO-based DBN (PSODBN), WOA-based NN (WOANN) techniques and the results are obtained, which shows the superiority of proposed algorithm over conventional methods.