Permeability is a physical property of rock masses and it is very important in difference field of engineering works, particularly in the Earth science. It is usually calculated with analytical and numerical methods. Analytical methods apply for simple and regular joint set systems and for complicated Discrete Fracture Network (DFN) models only numerical methods are applicable. Numerical simulations demand a large computation resources and great space for data storage and in general it is very time consuming particularly when we have a large model size with densely populated of fractures. Using Effective Medium Theory (EMT) approach for calculation the conductivity and permeability of a lattice network is also reported in the literature as alternative method for numerical solution. However the degree of uncertainties for fluid flow analysis using EMT method compared with numerical modeling has not yet been calculated and reported and is the main objective of this research work. Firstly, we developed a code based on the modified EMT methodology for calculating the overall permeability of fracture networks using Matlab program and Representative Elementary Volume (REV) sizes are also approximated. A sensitivity analysis about the effect of geometrical parameters of fracture distribution such as density, orientation fractures and also three different aperture patterns are considered; constant aperture, distributed fracture apertures are correlated/uncorrelated with trace length, were set for quantifying the degree of uncertainties between calculated permeability by numerical and EMT methods. Using Monte Carlo simulation techniques, stochastic DFN models were generated with a large number of realizations. The Universal Distinct Element Code (UDEC) is also facilitated for numerical simulation analysis. The results show that the calculated mean values of permeability between DFN realization models by EMT method are closely to the results of numerical methods particularly when the fracture density is large, in this work 6.9. The REV size for DFN models with constant fracture aperture are approximated in the same value, however, for distributed fracture aperture models the REV size in EMT method is smaller than numerical methods. The results of sensitivity analysis show that the effect of geometric parameters of fractures on calculated permeability with two methods follow the same trend. With increasing the fracture density network permeability is increased and concentration coefficient of fisher distribution of fracture orientation does not have a significant impact on the results.