Low-cost airlines have significantly increased air transport, thus an increase in aviation noise. Therefore, predicting aircraft noise is an important component for designing an aircraft to reduce its impact on environmental noise along with the cost of testing and certification. The aim of this work is to develop a three-dimensional Boundary Element Method (BEM), which can predict the sound propagation and scattering over metamaterials and metasurfaces in mean flow. A methodology for the implementation of metamaterials and metasurfaces in BEM as an impedance patch is presented here. A three-dimensional BEM named as BEM3D has been developed to solve the aero-acoustics problems, which incorporates the Fast Multipole Method to solve large scale acoustics problems, Taylor’s transformation to account for uniform and non-uniform mean flow, impedance and non-local boundary conditions for the implementation of metamaterials. To validate BEM3D, the predictions have been benchmarked against the Finite Element Method (FEM) simulations and experimental data. It has been concluded that for no flow case BEM3D gives identical acoustics potential values against benchmarked FEM (COMSOL) predictions. For Mach number of 0.1, the BEM3D and FEM (COMSOL) predictions show small differences. The difference between BEM3D and FEM (COMSOL) predictions increases further for higher Mach number of 0.2 and 0.3. The increase in difference with Mach number is because Taylor’s Transformation gives an approximate solution for the boundary integral equation. Nevertheless, it has been concluded that Taylor’s transformation gives reasonable predictions for low Mach number of up to 0.3. BEM3D predictions have been validated against experimental data on a flat plate and a duct. Very good agreement has been found between the measured data and BEM3D predictions for sound propagation without and with the mean flow at low Mach number.