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-of- the-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.