The Eocene aquifer is one of the major groundwater aquifers in Palestine. It is located in the northeastern part of the West Bank covering areas of both Jenin and Nablus districts. The development of the groundwater within the Eocene aquifer is very essential for the Palestinian water supply. This paper simulates for groundwater flow in the Eocene aquifer using MODFLOW as a strong available groundwater model. The groundwater budget, flow computation, and flow path-lines were estimated and calibrated. Groundwater balance has been evaluated. The Modeling results show that a minimum initial level of 340 m above sea level should be applied to model the hydraulics of the aquifer correctly. The recharge and hydraulic conductivity are the most sensitive model parameters. The hydraulic conductivity in some areas has proved to be double than assumed by other literatures. More reasonable recharge coefficients in comparison to other literatures have been obtained. Groundwater balance indicated that the water budget of the Eocene aquifer totals about 72 MCM/yr. The modeling has indicated reasonable matching between the observed and modeled groundwater levels and spring flows. The flow direction within the aquifer is from the south to north and northeast. The Faria spring system located to the southeast is the major sink within the aquifer. It attracts most of the particle tracking lines due to its high discharge rates. It is recommended to monitor the existing wells and springs permanently. It is also recommended to assess the effect of the faults and fractures on the hydraulic conductivity.