The synthesis, structure, and physical properties of Y5Ru2O12, a new member of the Ln5B2O12 class (Ln = lanthanide, B = Ru, Re, Mo) are reported. Single crystals of Y5Ru2O12 are synthesized using a high‐temperature, high‐pressure (700 °C, 200 MPa) hydrothermal method. The structure features edge‐sharing RuORu 1D chains of distorted RuO6 octahedra. The YOn (n = 6 and 7) polyhedral groups bridge RuORu chains across the unit cell by forming a complex 3D structure. The RuORu chains contain alternating shorter and longer RuRu distances along the chain. Single crystal neutron diffraction shows streak‐like diffuse scattering along the H‐direction, due to stacking faults. Temperature‐dependent anisotropic magnetic measurements reveal a broad feature over a wide temperature range, with a maximum at ≈70 K indicating potential short‐range ordering, with canted antiferromagnetic behavior below 30 K. The dominant magnetic interactions are antiferromagnetic with a large negative Weiss temperature θ ≈ −200 K. The compound has an effective magnetic moment that is anomalously large for this class of compounds (≈4 μB Ru−1), and a phenomenological spin Hamiltonian describing the unusual anisotropic magnetization of Y5Ru2O12 is proposed.