The shear lag has been studied for many years. Nevertheless, existing research gives a variety of stress concentration factors. Unlike the elementary beam theory, the application of load is not unique in reality. For example, concentrated load can be applied as point load or distributed load along the height of the web. This non-uniqueness may be a reason for the discrepancy of the stress concentration factors in the existing studies. The finite element method has been often employed for studying the effect of the shear lag. However, not many researches have taken into account the influence of the finite element mesh on the shear lag phenomenon, although stress concentration can be quite sensitive to the mesh employed in the finite element analysis. This may be another source for the discrepancy of the stress concentration factors. It also needs to be noted that much less studies seem to have been conducted for the shear lag effect on deflection while some design codes have formulas. The present study investigates the shear lag effect in a simply supported box girder by the three-dimensional finite element method using shell elements. The whole girder is modeled by shell elements, and extensive parametric study with respect to the geometry of a box girder is carried out. Not only stress concentration but also deflection is computed. The effect of the way load is applied and the dependency of finite element mesh on the shear lag are carefully treated. Based on the numerical results thus obtained, empirical formulas are proposed to compute stress concentration and deflection that includes the shear lag effect.