Measuring the surface deformation of asphalt pavement and acquiring the rutting condition is of great importance to transportation agencies. This paper proposes a rutting measuring method based on an unmanned aerial vehicle (UAV) mounted with Light Detection and Ranging (LiDAR). Firstly, an airborne LiDAR system is assembled and the data acquisition method is presented. Then, the method for point cloud processing and rut depth computation is presented and the results of field testing are discussed. Thirdly, to investigate error factors, the laser footprint positioning model is established and sensitivity analysis is conducted. Factors including flight height, LiDAR instantaneous angel, and ground inclination angle are discussed. The model was then implemented to obtain the virtual rut depth and to verify the accuracy of the field test results. The main conclusions include that the measurement error increases with the flight height, instantaneous angle, and angular resolution of the LiDAR. The inclination angle of the pavement surface has adverse impact on the measuring accuracy. The field test results show that the assembled airborne LiDAR system is more accurate when the rut depth is significant. The findings of this study pave the way for future exploration of rutting measurement with airborne LiDAR.