Research on electrocardiogram (ECG) signals has been actively undertaken to assess their value as a next generation user recognition technology, because they require no stimulation and are robust against forgery and modification. However, even within the same user, the heart rate and waveform of ECG signals will vary depending on physical activity, mental effects, and measurement time. Therefore, when data acquired across changes in the user state is used as registered data, an overfitting problem occurs due to data generalization, which degrades the recognition performance for newly acquired data. Therefore, in this paper, we propose parallel ensemble networks to solve the overfitting problem and prevent the degradation. First, ECG signals acquired in various environments are used as the input data of parallel convolutional neural networks (CNNs). Each CNN is set up with different parameters to detect different features. The ECG signals outputted from each network are classified for each subject, and then fused into one database to be used as registered data for retraining. Instead of fusing all the output signals from each network, only the ECG signals of Top-3 networks showing excellent performance are fused and composed of registered data. The reconstructed registered data are used for user recognition, by retraining with time independent comparison data in the CNN. The experimental results of comparing the proposed parallel ensemble networks with those of previous studies using the self-acquired actual ECG signals show that the proposed method achieves recognition performance higher than the previous studies, with an accuracy rate of 98.5%. INDEX TERMS ECG, biometrics, user recognition, various situations, parallel ensemble networks.