The estimation of queue length at a signalized intersection, while enormously valuable in traffic operation and management, presents a number of challenges to transportation. One area where traffic optimization and analysis is lacking is the ability to dynamically estimate queue length at intersections where only limited GPS trajectory data were recorded and saved. To solve this challenge, an integer-programming model was proposed to estimate queue length and guarantee the consistent reconstruction of shockwave propagation. The model was further evaluated by comparing the estimated queue length with observed queue length in every signal period based on simulation data. The evaluation results not only demonstrate that the proposed model can estimate queue length, but also indicates the required penetration rate of floating vehicles.