The Finite Element Analysis (FEA) is evidently a powerful tool for the analysis of structural concrete having nonlinearity and brittle failure properties. However, the result of FEA of structural concrete is sensitive to two modeling factors: the shear transfer coefficient (STC) for an open concrete crack and force convergence tolerance value (CONVTOL). Very limited work has been done to find the optimal FE Modeling (FEM) methodologies for structural concrete members strengthened with externally bonded FRP sheets. A total of 22 experimental deep beams with or without FRP flexure or/and shear strengthening systems are analyzed by nonlinear FEA using ANAYS program. For each experimental beams, an FE model with a total of 16 cases of modeling factor combinations are developed and analyzed to find the optimal FEM methodology. Two elements the SHELL63 and SOLID46 representing the material properties of FRP laminate are investigated and compared. The results of this research suggest that the optimal combination of modeling factor is STC of 0.25 and CONVTOL of 0.2. A SOLID 46 element representing the FRP strengthening system leads to better results than a SHELL 63 element does.