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Accepted at IEEE ICNP HDR-Nets workshop 2020; Network traffic classification is an important task in modern communications. Several approaches have been proposed to improve the performance of differentiating among applications. However, most of them are based on supervised learning where only labeled data are used. In reality, a lot of datasets are partially labeled due to many reasons and unlabeled portions of the data, which can also provide informative characteristics, are ignored. To handle this issue, we propose a semi-supervised approach based on deep learning. We deployed deep learning because of its unique nature for solving problems, and its ability to take into account both labeled and unlabeled data. Moreover, it can also integrate feature extraction and classification into a single model. To achieve these goals, we propose an approach using stacked sparse autoencoder (SSAE) accompanied by de-noising and dropout techniques to improve the robustness of extracted features and prevent the over-fitting problem during the training process. The obtained results demonstrate a better performance than traditional models while keeping the whole procedure automated.