We present a deep learning-based method for super-resolving coarse (low-resolution) labels assigned to groups of image pixels into pixel-level (high-resolution) labels, given the joint distribution between those low- and high-resolution labels. This method involves a novel loss function that minimizes the distance between a distribution determined by a set of model outputs and the corresponding distribution given by low-resolution labels over the same set of outputs. This setup does not require that the high-resolution classes match the low-resolution classes and can be used in high-resolution semantic segmentation tasks where high-resolution labeled data is not available. Furthermore, our proposed method is able to utilize both data with low-resolution labels and any available high-resolution labels, which we show improves performance compared to a network trained only with the same amount of high-resolution data. We test our proposed algorithm in a challenging land cover mapping task to super-resolve labels at a 30m resolution to a separate set of labels at a 1m resolution. We compare our algorithm with models that are trained on high-resolution data and show that 1) we can achieve similar performance using only low-resolution data; and 2) we can achieve better performance when we incorporate a small amount of high-resolution data in our training. We also test our approach on a medical imaging problem, resolving low-resolution probability maps into high-resolution segmentation of lymphocytes with accuracy equal to that of fully supervised models.