We present the numerical modeling of field amplitude perturbations for two VLF/LF transmitters (JJI: 22.2 kHz, JJY: 40.0 kHz) signals recorded at six places (UEC-VLF network) in Japan during the Annular Solar Eclipse of 2012 (ASE-2012). We determine the characteristics of the D-region ionospheric perturbation according to the antumbra and penumbral shadow of the annular solar eclipse. A space–time dependent 2-Dimensional Elliptical Gaussian distribution Model (2DEGM) is introduced to get the effect of ASE-2012 on the Wait’s D-region parameters, such as effective VLF/LF reflection height (h′) and sharpness factor (β). The Long Wave Propagation Capability (LWPC) code is used to simulate the VLF signal amplitude profile with the help of modelled Wait’s parameters. A method of comparison of observed and LWPC simulated VLF signal amplitude across all the considered signal propagation paths is introduced to estimate final 2DEGM related parameters and hence, to model D-region electron density perturbations during ASE-2012. Using 2DEGM + LWPC, (i) we consistently simulate the observed VLF signal amplitude profiles for almost all the propagation paths of UEC-VLF network and (ii) evaluate the percentage change in D-region electron density due to ASE-2012.