Zeolite N is a synthetic zeolite of the EDI framework type with chemical formula K12Al10Si10O40Cl2·8H2O Experimental and computational investigations verify the valuable ion-exchange capability of zeolite N. In this study, we assess the effects of Local Density Approximation (LDA) and Generalized Gradient Approximation (GGA) DFT models on zeolite structural parameters and on partial atomic charges of framework atoms. We applied these functionals with different quality of convergence and SCF tolerances, numerical basis sets and dispersion correction schemes. Optimized zeolite N structures are evaluated by comparing the atom positions and framework T—O bond lengths with experimental data. The obtained Si—O and A—O bond lengths of optimized structures in this study are in agreement with previous experimental and computational studies on zeolite N and other zeolites. The values of Mulliken partial atomic charges are sensitive to the choice of numerical basis sets. Results show that the GGA-PBE functional with DNP-4.4 basis set and TS dispersion correction scheme is a reliable DFT model in order to optimize and establish the structural parameters of zeolite N for further MD simulations.