The Particle Finite Element Method (PFEM) is widely used for the explicit simulation of highly nonlinear fluid dynamics and fluid–structure interaction problems. However, standard PFEM formulations rely on frequent remeshing strategies that may introduce artificial mass variation, mesh distortion, and time-step restrictions, particularly in three-dimensional applications. This work presents Cut-PVEM, a novel boundary treatment strategy for explicit PFEM that combines robust geometric mesh cutting with agglomeration techniques inspired by the Particle Virtual Element Method. Fluid–boundary interactions are detected through explicit local geometric operations: elements intersected by solid boundaries are cut and subsequently agglomerated into polyhedral Virtual Elements, which naturally support arbitrary shapes, nonconvex geometries, and variable connectivity without mesh optimization or interface elements. By exploiting the agglomeration capabilities of the Virtual Element Method, Cut-PVEM avoids the generation of sliver elements typically associated with three-dimensional remeshing and boundary reconstruction techniques. The characteristic length of the agglomerated elements can be effectively controlled, ensuring stable time-step sizes in explicit dynamics. In addition, the proposed approach inherently prevents artificial mass creation and eliminates contact time anticipation. Numerical results in two and three dimensions demonstrate that Cut-PVEM provides a robust, accurate, and computationally efficient framework for the simulation of weakly compressible flows with complex and evolving boundaries.