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Segmentation of objects of interest is one of the central tasks in medical image analysis, which is indispensable for quantitative analysis. When developing machine-learning based methods for automated segmentation, manual annotations are usually used as the ground truth toward which the models learn to mimic. While the bulky parts of the segmentation targets are relatively easy to label, the peripheral areas are often difficult to handle due to ambiguous boundaries and the partial volume effect, etc., and are likely to be labeled with uncertainty. This uncertainty in labeling may, in turn, result in unsatisfactory performance of the trained models. In this paper, we propose superpixel-based label softening to tackle the above issue. Generated by unsupervised over-segmentation, each superpixel is expected to represent a locally homogeneous area. If a superpixel intersects with the annotation boundary, we consider a high probability of uncertain labeling within this area. Driven by this intuition, we soften labels in this area based on signed distances to the annotation boundary and assign probability values within [0, 1] to them, in comparison with the original "hard", binary labels of either 0 or 1. The softened labels are then used to train the segmentation models together with the hard labels. Experimental results on a brain MRI dataset and an optical coherence tomography dataset demonstrate that this conceptually simple and implementation-wise easy method achieves overall superior segmentation performances to baseline and comparison methods for both 3D and 2D medical images.