Recent user recognition technologies have focused on biometric signals to remotely identify users in the access management, medical welfare, and public sectors. The electrocardiogram (ECG) signal is an individual's unique electrophysiological signal generated within the body and is difficult to forge or change; thus, it can be used to uniquely identify the user. Existing user identification systems based on ECG signals detect R peaks according to morphological features and use a fiducial-based segmentation process for data normalization. However, this process does not detect a distinct R peak due to motion artifacts generated by the movement of the subject, thereby degrading identification accuracy. To address the problem of decreasing peak accuracy of the fiducial-based segmentation data, this study proposes a user identification system based on one-dimensional neural networks using periodic non-fiducial-based segmentation data that do not overlap in the time domain. The proposed system comprises a preprocessing step for data denoising, a non-fiducial-based and non-overlap segmentation step, and a step for classifying users using a one-dimensional shallow neural network. In the experiment, when using self-acquired 10-second ECG signal data that were divided into non-fiducial and non-overlapping segments, the long short-term memory (LSTM), bidirectional LSTM, and one-dimensional convolutional neural network (CNN) models achieved accuracies of 92.01%, 93.13%, and 95.51%, respectively, with the 1D CNN model exhibiting the best accuracy. The proposed system demonstrated a 25.48% improvement in accuracy on non-fiducial segmented data compared to the 1D CNN model, which achieved an accuracy of 70.03% on fiducial segmented data. Moreover, when tested on publicly available ECG datasets, including MIT-BIH, ECG-ID, and PTB-XL, the proposed system exhibited a user identification accuracy of over 94%, confirming its superior performance.