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Instance segmentation, which seeks to obtain both class and instance labels for each pixel in the input image, is a challenging task in computer vision. State-ofthe-art algorithms often employ a search-based strategy, which first divides the output image with a regular grid and generate proposals at each grid cell, then the proposals are classified and boundaries refined. In this paper, we propose a novel algorithm that directly utilizes a fully convolutional network (FCN) to predict instance labels. Specifically, we propose a variational relaxation of instance segmentation as minimizing an optimization functional for a piecewise-constant segmentation problem, which can be used to train an FCN end-to-end. It extends the classical Mumford-Shah variational segmentation algorithm to be able to handle the permutation-invariant ground truth in instance segmentation. Experiments on PASCAL VOC 2012 and the MSCOCO 2017 dataset show that the proposed approach efficiently tackles the instance segmentation task. The source code and trained models are released at https://github.com/jia2lin3yuan1/2020-instanceSeg.