Electroencephalogram (EEG) signals immensely suffer from several physiological artifacts, including electrooculogram (EOG), electromyogram (EMG), and electrocardiogram (ECG) artifacts, which must be removed to ensure EEG’s usability. This paper proposes a novel one-dimensional convolutional neural network (1D-CNN), i.e., MultiResUNet3+, to denoise physiological artifacts from corrupted EEG. A publicly available dataset containing clean EEG, EOG, and EMG segments is used to generate semi-synthetic noisy EEG to train, validate and test the proposed MultiResUNet3+, along with four other 1D-CNN models (FPN, UNet, MCGUNet, LinkNet). Adopting a five-fold cross-validation technique, all five models’ performance is measured by estimating temporal and spectral percentage reduction in artifacts, temporal and spectral relative root mean squared error, and average power ratio of each of the five EEG bands to whole spectra. The proposed MultiResUNet3+ achieved the highest temporal and spectral percentage reduction of 94.82% and 92.84%, respectively, in EOG artifacts removal from EOG-contaminated EEG. Moreover, compared to the other four 1D-segmentation models, the proposed MultiResUNet3+ eliminated 83.21% of the spectral artifacts from the EMG-corrupted EEG, which is also the highest. In most situations, our proposed model performed better than the other four 1D-CNN models, evident by the computed performance evaluation metrics.