Semantic segmentation is one of the popular tasks in computer vision, providing pixel-wise annotations for scene understanding. However, segmentation-based convolutional neural networks require tremendous computational power. In this work, a fully-pipelined hardware accelerator with support for dilated convolution is introduced, which cuts down the redundant zero multiplications. Furthermore, we propose a genetic algorithm based automated channel pruning technique to jointly optimize computational complexity and model accuracy. Finally, hardware heuristics and an accurate model of the custom accelerator design enable a hardware-aware pruning framework. We achieve 2.44X lower latency with minimal degradation in semantic prediction quality (−1.98 pp lower mean intersection over union) compared to the baseline DeepLabV3+ model, evaluated on an Arria-10 FPGA. The binary files of the FPGA design, baseline and pruned models can be found in github.com/pierpaolomori/SemanticSegmentationFPGA.