We report the experimental observation of two-dimensional (2D) quantum Griffiths singularity (QGS) in ∼200-nm-thick epitaxial ZrNₓ superconducting films. The films possess a rock-salt structure and are three-dimensional (3D) with respect to superconductivity. For each film with x ≳ 1.30, the low-temperature magnetoresistance isotherms under fields perpendicular and parallel to the film plane cross over at a broad magnetic field range independently rather than at a single crossing point. Despite the macroscopic 3D nature of the superconductivity, the magnetoresistance isotherms at selected adjacent temperatures follow the theoretical prediction of power-law scaling for 2D superconducting systems, rather than that for 3D systems. The effective critical exponent zν, obtained by analyzing the magnetoresistance isotherms using the 2D power-law scaling, increases with decreasing temperature and diverges as the quantum phase transition is approached. In addition, the resistivity data near the superconductor-insulator or superconductor-metal transitions obey an activated scaling form that describes the quantum phase transition of 2D superconducting systems governed by an infinite-randomness critical point. The QGS in the ZrNₓ films is attributed to quenched disorder induced by intrinsic defects, such as Zr vacancies and N interstitials, which creates spatially inhomogeneous superconducting rare regions. The dynamics of these rare regions, which may exhibit effective 2D characteristics near the quantum critical point, dominate the transport properties of the system near the quantum phase transition. Our results provide compelling evidence for the existence of QGS in 3D superconductors and highlight the crucial role of disorder-induced inhomogeneity in determining the critical behavior of quantum phase transitions.