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In this paper, a multihypothesis-based centralized Failure Diagnosis in Protection System (FDProSys) tool using phasor measurement units (PMU) data has been proposed to systematically and automatically detect malfunctions or failures in protective devices. The proposed diagnostic algorithm and FDProSys tool employs synchrophasor measurements to select a section of the network called ProNet, with possible device malfunction. Multiple hypotheses have been generated automatically based on node incidence matrices and multihypothesis theory. The malfunction of the protective devices in the presence of fault and relay operation is identified by comparing the five-digit message of the real event with multiple hypotheses. Trustworthiness of PMU data caused by common failures, such as communication outage and GPS problems, has also been considered by the proposed algorithm using the PMU status flag. The developed tool FDProSys can also work with supervisory control and data acquisition data assisted by manual analysis with less accuracy and is robust enough to several PMU/relay failures. Simulation results using the IEEE 14-bus, IEEE 57-bus, and IEEE 300-bus systems demonstrate the accuracy of the developed algorithm. [ABSTRACT FROM AUTHOR]