The fundamental diagram (FD), also known as the flow-density relation, is one of the most fundamental concepts in the traffic flow theory. Conventionally, FDs are estimated by using data collected by detectors. However, detectors' installation sites are generally limited due to their high cost, making practical implementation of traffic flow theoretical works difficult. On the other hand, probe vehicles can collect spatially continuous data from wide-ranging area, and thus they can be useful sensors for large-scale traffic management. In this study, a novel framework of FD estimation by using probe vehicle data is developed. It determines FD parameters based on trajectories of randomly sampled vehicles and a given jam density that is easily inferred by other data sources. A computational algorithm for estimating a triangular FD based on actual, potentially noisy traffic data obtained by multiple probe vehicles is developed. The algorithm was empirically validated by using real-world probe vehicle data on a highway. The results suggest that the algorithm accurately and robustly estimates the FD parameters.