A three-dimensional finite-difference groundwater flow model was developed by the use of fractal theory. The model developed in this study can simulate the groundwater flow in fractured aquifers as well as in porous aquifers. The model was designed to be able to use other parameters, such as permeability, hydraulic conductivity, porosity and fractal dimension besides hydraulic parameters which are used in MODFLOW. Methods which can calculate box fractal dimension used in the Baecher model and mass dimension used in Levy-Lee Fractal model were developed. The results of the model and MODFLOW agreed exactly in the case of the fractal dimension of 2.0 without regard to the use of a fractal equation. The fact that the drawdown along the distance from the well increases by increasing the fractal dimension shows the effect of fracture on groundwater flow.