This study investigated the hydrodynamics of a solitary wave passing a vertical cylinder over a viscous mud bed for the first time. A highly viscous Newtonian fluid was assumed as a simplified model for fluid mud. A three-dimensional numerical wave flume consisting of a fixed cylindrical structure and three viscous fluids—air, water, and mud—was constructed and validated. Numerical experiments were performed to investigate solitary wave interaction with a vertical cylinder over a viscous mud bed. Numerical results showed the mud surface deformation to be one order of magnitude smaller than the water surface deformation and their behaviors to be different: mud surface depressions occurred on the upstream and downstream sides of the cylinder, whereas mud surface elevations occurred on the lateral sides of the cylinder. This solitary wave induced scour pattern on a muddy seabed is different from that commonly observed on a sandy seabed. Water flow reversal near the water–mud interface was made more evident by the mud bed. Although the mud bed attenuated water waves, it nevertheless increased the total horizontal force and toppling moment exerted on the cylinder due to the wave-induced mud flow. These findings may be valuable to the design of marine structures on a muddy seabed and worthy of further investigation.