An electrocardiogram (ECG) is a unique representation of a person’s identity, similar to fingerprints, and its rhythm and shape are completely different from person to person. Cloning and tampering with ECG-based biometric systems are very difficult. So, ECG signals have been used successfully in a number of biometric recognition applications where security is a top priority. The major challenges in the existing literature are (i) the noise components in the signals, (ii) the inability to automatically extract the feature set, and (iii) the performance of the system. This paper suggests a beat-based template matching deep learning (DL) technique to solve problems with traditional techniques. ECG beat denoising, R-peak detection, and segmentation are done in the pre-processing stage of this proposed methodology. These noise-free ECG beats are converted into gray-scale images and applied to the proposed deep-learning technique. A customized activation function is also developed in this work for faster convergence of the deep learning network. The proposed network can extract features automatically from the input data. The network performance is tested with a publicly available ECGID biometric database, and the proposed method is compared with the existing literature. The comparison shows that the proposed modified Siamese network authenticated biometrics have an accuracy of 99.85%, a sensitivity of 99.30%, a specificity of 99.85%, and a positive predictivity of 99.76%. The experimental results show that the proposed method works better than the state-of-the-art techniques.