The Shear Lag Effect (SLE) is one of the vital mechanical characteristics of structures with thinwalled box section. While most of the existing studies on SLE focus on the static response of footbridges, the pedestrian-induced vibration deserves more attention since it represents the actual response of footbridges during their practical service process. The theoretical framework is proposed to consider the corresponding SLE. Firstly, the SLE on the natural frequencies of the structure can be considered with a reduction ratio to the corresponding case without considering SLE (the classic solutions of natural frequencies). Results show that, the footbridges with smaller span-width ratios, smaller section thickness-width ratios, and lower height-width ratios are more necessary to consider the SLE. Furthermore, although the Poisson's ratio effects are relatively lower than other aspects, the steel bridges still need to be paid to attention for the SLE. Due to the SLE, it may result in significant reductions in the natural frequencies of the structures. These reductions in the predicted natural frequencies due to the SLE may further result in inaccuracy in the prediction of pedestrian-induced vibrations of the footbridges. Furthermore, the most often applied mitigation measures may not be reliably designed. It may result in very significant reduction in the effectiveness of the vibration mitigation measures. To consider the SLE on pedestrian-induced vibration and TMD-based vibration control of typical footbridges with thin-walled box section, a simplified strategy is proposed.