While in standard clustering no side information is used, users might be interested in providing additional information to influence the clustering. In case of document clustering, additional information can take the form of pairwise constraints where a user provides additional information about pairs of documents as must-link and cannot-link constraints (indicating respectively whether the documents in the pair are coming from the same cluster or not). In this paper, we propose a novel deep document clustering framework which can employ pairwise constraints while learning document representations to obtain better tailored results. Indeed, in our proposed framework, data representations (obtained through an autoencoder) and cluster representatives are learned through back propagation in a joint way. Devising a fully differentiable deep clustering framework with the ability of using pairwise constraints is the main contribution of this paper. Experiments conducted on 5 public datasets show the gain in clustering performance which the resulting approach can yield.