Traditional Japanese orchards control the growth height of fruit trees for the convenience of farmers, which is unfavorable to the operation of medium- and large-sized machinery. A compact, safe, and stable spraying system could offer a solution for orchard automation. Due to the complex orchard environment, the dense tree canopy not only obstructs the GNSS signal but also has effects due to low light, which may impact the recognition of objects by ordinary RGB cameras. To overcome these disadvantages, this study selected LiDAR as a single sensor to achieve a prototype robot navigation system. In this study, density-based spatial clustering of applications with noise (DBSCAN) and K-means and random sample consensus (RANSAC) machine learning algorithms were used to plan the robot navigation path in a facilitated artificial-tree-based orchard system. Pure pursuit tracking and an incremental proportional–integral–derivative (PID) strategy were used to calculate the vehicle steering angle. In field tests on a concrete road, grass field, and a facilitated artificial-tree-based orchard, as indicated by the test data results for several formations of left turns and right turns separately, the position root mean square error (RMSE) of this vehicle was as follows: on the concrete road, the right turn was 12.0 cm and the left turn was 11.6 cm, on grass, the right turn was 12.6 cm and the left turn was 15.5 cm, and in the facilitated artificial-tree-based orchard, the right turn was 13.8 cm and the left turn was 11.4 cm. The vehicle was able to calculate the path in real time based on the position of the objects, operate safely, and complete the task of pesticide spraying.