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The electrocardiogram (ECG) is an efficient and noninvasive indicator for arrhythmia detection and prevention. In real-world scenarios, ECG signals are prone to be contaminated with various noises, which may lead to wrong interpretation. Therefore, significant attention has been paid on denoising of ECG for accurate diagnosis and analysis. A denoising autoencoder (DAE) can be applied to reconstruct the clean data from its noisy version. In this paper, a DAE using the fully convolutional network (FCN) is proposed for ECG signal denoising. Meanwhile, the proposed FCN-based DAE can perform compression with regard to the DAE architecture. The proposed approach is applied to ECG signals from the MIT-BIH Arrhythmia database and the added noise signals are obtained from the MIT-BIH Noise Stress Test database. The denoising performance is evaluated using the root-mean-square error (RMSE), percentage-root-mean-square difference (PRD), and improvement in signal-to-noise ratio (SNR <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">imp</sub> ). The results of the experiments conducted on noisy ECG signals of different levels of input SNR show that the FCN acquires better performance as compared to the deep fully connected neural network- and convolutional neural network-based denoising models. Moreover, the proposed FCN-based DAE reduces the size of the input ECG signals, where the compressed data is 32 times smaller than the original. The results of the study demonstrate the superiority of FCN in denoising, with lower RMSE and PRD, as well as higher SNR <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">imp</sub> . According to the results, we believe that the proposed FCN-based DAE has a good application prospect in clinical practice.