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Fluid injection associated with geoenergy applications such as geothermal energy, CO2 sequestration, and hydraulic fracturing can alter fault stability through a combination of coupled hydro-mechanical processes. Laboratory experiments and underground observatories have provided valuable constraints on fault friction and near-fault pressure evolution, yet translating these observations to field-scale behavior requires physics-based numerical models that can resolve fault slip under realistic geometrical and mechanical conditions.A major limitation of existing modeling approaches is the high computational cost of fully coupled three-dimensional simulations. As a result, many studies rely on one-dimensional fault representations or simplified elastic and hydraulic coupling. While such models have provided important insights into key physical mechanisms, they are not well suited to support the design, interpretation, and long-term forecasting of modern injection experiments equipped with dense monitoring systems. These experimental settings increasingly demand three-dimensional models capable of capturing realistic fault geometry, spatially variable frictional and hydraulic properties, and stress interactions beyond reduced-dimensional assumptions.Here we present HydroMech3D, a physics-based numerical framework designed to efficiently simulate fluid-driven fault slip over earthquake-cycle timescales in three dimensions. The model employs a quasi-dynamic Boundary Element Method, discretizing only the fault surface embedded in elastic medium, thereby avoiding volumetric meshing. Fault slip is governed by rate-and-state friction and coupled to pore-pressure diffusion along the fault. Computational efficiency is achieved through a C++ implementation accelerated by hierarchical matrix from the Bigwham Library, enabling large-scale simulations with realistic fault geometry.This framework allows systematic investigation of fault-scale heterogeneity, including asperities with contrasting frictional and hydraulic properties, and provides a platform to explore how three-dimensional fault structure influences aseismic slip, stress transfer, and earthquake nucleation during fluid injection. Benchmarking against established earthquake-cycle test cases validates the mechanical solver and establishes a baseline for ongoing fully coupled simulations. HydroMech3D offers a computationally efficient open-source tool to support experiment design, interpretation of near-fault observations, and assessment of induced seismicity in geoenergy applications.