3D semantic occupancy prediction is essential for achieving safe, reliable autonomous driving and robotic navigation. Compared to camera-only perception systems, multi-modal pipelines, especially LiDAR-camera fusion methods, can produce more accurate and fine-grained predictions. Although voxel-based scene representations are widely used for semantic occupancy prediction, 3D Gaussians have emerged as a continuous and significantly more compact alternative. In this work, we propose a multi-modal Gaussian-based semantic occupancy prediction framework utilizing 3D deformable attention, namely GaussianFormer3D. We introduce a voxel-to-Gaussian initialization strategy that provides 3D Gaussians with accurate geometry priors from LiDAR data, and design a LiDAR-guided 3D deformable attention mechanism to refine these Gaussians using LiDAR-camera fusion features in a lifted 3D space. Extensive experiments on real-world on-road and off-road autonomous driving datasets demonstrate that GaussianFormer3D achieves state-of-the-art prediction performance with reduced memory consumption and improved efficiency.