Due to advancements in healthcare monitoring systems, the Internet of Things concepts are proficiently utilized in the medical field to detect and diagnose the physical health problems. The compression of more substantial medical information is a significant issue that requires ample data storage space and takes longer transmission time. Though several compression algorithms are actualized in past cases, there is an absence of an upgraded approach to achieve improved signal compression without influencing signal quality. Hence a proficient signal compression algorithm is proposed in our work to provide an enhanced electrocardiogram (ECG) signal compression without any data loss and to acquire increased compression ratio (CR) and zero construction error. In this proposed approach, the input ECG signal dataset from the MIT‐BIH arrhythmia database gets influenced by noise because of the electrical measuring gadget. Hence, preprocessing is done by the proposed multi‐scoop notch filter (MSNF) to denoise this signal by removing the specified noise frequency range of around (1‐50) Hz. This proposed MSNF is designed with adaptiveness that has achieved the enhanced denoising by adjusting the notch frequency. In addition, to extricate the sophisticated ECG signal features, Fast Fourier Transform is being utilized, and that performs and decomposes the signal elegantly and obtains characteristics of the signal in the frequency domain. After feature extraction, optimal signal compression is performed by our proposed priority‐based convolutional auto‐encoder (PCAE) that provides better compression with almost zero reconstruction error by encoding the signals into lower‐dimensional vectors in convolutional layers which are again reconstructed using a decoding approach. The experimental results are then assessed using the performance metrics that include signal to noise ratio (SNR), CR, and percentage root‐mean‐square difference (PRD). The attained results are 1.83% as average PRD value, average SNR is about 33 dB, and average CR is about 35.2% whereas the traditional CAE approach has average values of 2.05% PRD, 23.45 dB SNR, and 32.2% CR.