Many low-lying tropical and subtropical reef-fringed coasts are vulnerable to inundation during tsunami events. Hence accurate prediction of tsunami wave transformation and run-up over such reefs is a primary concern in the coastal management of hazard mitigation. To overcome the deficiencies of using depth-integrated models in modeling tsunami-like solitary waves interacting with fringing reefs, a three-dimensional (3-D) numerical wave tank based on the computational fluid dynamics (CFD) tool OpenFOAM^® is developed in this study. The Navier–Stokes equations for two-phase incompressible flow are solved, using the large eddy simulation (LES) method for turbulence closure and the volume-of-fluid (VOF) method for tracking the free surface. The adopted model is firstly validated by two existing laboratory experiments with various wave conditions and reef configurations. The model is then applied to examine the impacts of varying reef morphologies (fore-reef slope, back-reef slope, lagoon width, reef-crest width) on the solitary wave run-up. The current and vortex evolutions associated with the breaking solitary wave around both the reef crest and the lagoon are also addressed via the numerical simulations.