This work presents a novel photo-electrochemical architecture based on the 3D pyramid-like graphene/p-Si Schottky junctions. Overcoming the conventional transfer technique by which only planar graphene/Si Schottky junctions are currently available, this work demonstrates the 3D pyramid-like graphene/p-Si Schottky junction photocathode, which greatly enhances light harvesting efficiency and exhibits promising photo-electrochemical performance for hydrogen generation. The formation of 3D pyramid-like graphene/p-Si Schottky junctions exhibits enhanced electrochemical activity and promotes charge separation efficiency compared with the bare pyramid Si surface without graphene. The inherent chemical inertness of graphene significantly improves the operational stability of 3D graphene/p-Si Schottky junction photo-electrochemical cells. The 3D pyramid-like graphene/p-Si Schottky junction photocathode delivers an onset potential of 0.41 V and a saturated photocurrent density of −32.5 mA cm−2 at 0 V (vs RHE) with excellent stability comparable to values reported for textured or nanostructured p-Si photocathodes coated with ultrathin oxide layers by the conventional atomic layer deposition technique. These results suggest that the formation of graphene/Si Schottky junctions with a 3D architecture is a promising approach to improve the performance and durability of Si-based photo-electrochemical systems for water splitting or solar-to-fuel conversion.