An analytical method considering axial equilibrium is proposed for the short- and long-term analyses of shear lag effect in reinforced concrete (RC) box girders. The axial equilibrium of box girders is taken into account by using an additional generalized displacement, referred to as the longitudinal displacement of the web. Three independent shear lag functions are introduced to describe different shear lag intensities of the top, bottom, and cantilever plates. The time-dependent material properties of the concrete are simulated by the age-adjusted effective modulus method (AEMM), while the reinforcement is assumed to behave in a linear-elastic fashion. The differential equations are derived based on the longitudinal displacement of the web, the vertical displacement of the cross section, and the shear lag functions of the flanges. The time-dependent expressions of the generalized displacements are then deduced for box girders subjected to uniformly distributed loads. The accuracy of the proposed method is validated against the finite element results regarding the short- and long-term responses of a simply-supported RC box girder. Furthermore, creep analyses considering and neglecting shrinkage are performed to quantify the time effects on the long-term behavior of a continuous RC box girder. The results show that the proposed method can well evaluate both the short- and long-term behavior of box girders, and that concrete shrinkage has a considerable impact on the concrete stresses and internal forces, while concrete creep can remarkably affect the long-term deflections.