This paper aims at developing numerically validated models for predicting the through-plane effective index of refraction and absorption index of nanocomposite thin films. First, models for the effective optical properties of such materials are derived from previously reported analysis applying the volume averaging theory (VAT) to Maxwell’s equations. The transmittance and reflectance of nanoporous thin films are computed by solving Maxwell’s equations and the associated boundary conditions at all interfaces using finite element methods. The effective optical properties of the films are retrieved by minimizing the root mean square of the relative errors between the computed and theoretical transmittance and reflectance. Nanoporous thin films made of SiO2 and TiO2 consisting of cylindrical nanopores and nanowires are investigated for different diameters and various porosities. Similarly, electromagnetic wave transport through dielectric medium with embedded metallic nanowires are simulated. The numerical results are compared with predictions from widely used effective property models including (1) the Maxwell-Garnett theory, (2) the Bruggeman effective medium approximation, (3) the parallel, (4) series, (5) Lorentz-Lorenz, and (6) the VAT models. Very good agreement is found with the VAT model for both the effective index of refraction and absorption index. Finally, the effect of volume fraction on the effective index of refraction and absorption index predicted by the VAT model is discussed. For certain values of wavelengths and volume fractions, the effective index of refraction or absorption index of the composite material can be smaller than that of both the continuous and dispersed phases. These results indicate guidelines for designing nanocomposite materials with desired optical properties.