The tremendous development of the Internet of Things (IoT) technology in the last decades has fostered advancement in automatic medical assistive devices to support the existing Electronic Health Record (EHR) system. As an integral part of the EHR electronic model, public cloud servers store medical data. Unfortunately, public cloud servers are prone to security and privacy breach. This paper introduces a novel non-cryptographic approach to preserve electrocardiograph (ECG) data confidentiality and integrity in the EHR environment. The main objective of the proposed anonymization algorithm is to obscure the patient’s cardiac information during transmission and to protect information stored in the cloud database. Although we focus on ECG data, generalization to other types of clinical data can be derived using the proposed method. Performance evaluation of the proposed scheme showed that the algorithm conceals both fiducial and non-fiducial features of the data. Therefore, confidentiality feature is preserved. This paper examined confidentiality of the anonymized data using the Percentage Residual Difference (PRD) and investigated the integrity of the reconstructed data in terms of cross-correlation. Security analysis carried out using the PRD, brute force attack, and performance comparison between the proposed algorithm and existing methods. Evaluation showed that the proposed scheme offers a secure non-cryptographic model for transmission and storing clinical data in the cloud. Moreover, in terms of processing time, the proposed algorithm is ten times faster than the existing wavelet packet method when processing long ECG data, 65,536 sample points. In a real-time experimental testbed, the implemented proposed system was successful.