Semantic segmentation plays a significant role in unstructured and planetary scene understanding, offering to a robotic system or a planetary rover valuable knowledge about its surroundings. Several studies investigate rover-based scene recognition planetary-like environments but there is a lack of a semantic segmentation architecture, focused on computing systems with low resources and tested on the lunar surface. In this study, a lightweight encoder-decoder neural network (NN) architecture is proposed for rover-based ground segmentation on the lunar surface. The proposed architecture is composed by a modified MobilenetV2 as encoder and a lightweight U-net decoder while the training and evaluation process were conducted using a publicly available synthetic dataset with lunar landscape images. The proposed model provides robust segmentation results, allowing the lunar scene understanding focused on rocks and boulders. It achieves similar accuracy, compared with original U-net and U-net-based architectures which are 110–140 times larger than the proposed architecture. This study, aims to contribute in lunar landscape segmentation utilizing deep learning techniques, while it proves a great potential in autonomous lunar navigation ensuring a safer and smoother navigation on the moon. To the best of our knowledge, this is the first study which propose a lightweight semantic segmentation architecture for the lunar surface, aiming to reinforce the autonomous rover navigation.