Chronic kidney disease (CKD) is a prominent disease that causes loss of functionality in the kidney. Doctors can now more easily gather patient health status data due to the growth of the Internet of Health Things (IoHT). The IoHT data contains a huge number of redundant data, making it challenging to predict CKD disease quickly and accurately. In healthcare applications like feature-based classification, a variety of disease diagnosis systems were used to address this problem. Current disease detection algorithms suffer from imbalanced dataset processing, low-accuracy feature learning, and high computational power requirements. Thus, deep learning-based clinical decision support systems have been developed to solve these complexities. To remove outliers from medical data, data collected with IoHT devices is first pre-processed using an enhanced K-means clustering technique. The Synthetic Minority over Sampling Technique is used to balance data because the IoHT dataset is highly imbalanced. The classifier detects anomalies in less time because of the implemented processing step. The balanced CKD dataset is then presented for use with a novel classifier called Residual Attention-Gated Autoencoder with Support Vector Machine. In order to improve accurate detection, the adopted classifier can learn and extract features. The proposed method results in an increased accuracy of 99.43% within 70.1 s of computation time. The mean intersection of the union and kappa coefficient of the proposed method is 98.15% and 98.1%, respectively.