Non-invasive fetal electrocardiography represents a valuable alternative continuous fetal monitoring method that has recently received considerable attention in assessing fetal health. However, the non-invasive fetal electrocardiogram (ECG) is typically severely contaminated by a considerable amount of various noise sources, rendering fetal ECG denoising a very challenging task. This work employs a deep learning approach for removing the residual noise from multi-channel fetal ECG after the maternal ECG has been suppressed. We propose a deep convolutional encoder-decoder network with symmetric skip-layer connections, learning end-to-end mappings from noise-corrupted fetal ECG signals to clean ones. Experiments on simulated data show an average signal-to-noise ratio (SNR) improvement of 9.5 dB for fetal ECG signals with input SNR ranging between −20 and 20 dB. The method is additionally evaluated on a large set of real signals, demonstrating that it can provide significant quality improvement of the noisy fetal ECG signals. We further show that employment of multi-channel signal information by the network provides superior and more reliable performance as opposed to its single-channel network counterpart. The presented method is able to preserve beat-to-beat morphological variations and does not require any prior information on the power spectra of the noise or the pulse location.