This study proposes a binary search-based fault detection system for photovoltaic (PV) modules to ameliorate the deficiencies in the existing fault detectors for PV module arrays. The proposed system applies a single-chip microcontroller to execute the binary search algorithm. Moreover, to overcome multi-node voltage detection and reduce the number of integrated circuit components, an analog switch is used to perform detection channel switching; the detection results are displayed on a software platform developed using Visual C#. The proposed system does not require learning to execute the fault diagnosis of PV module arrays and has advantages including high accuracy and low construction costs. Finally, to verify the feasibility of the proposed system, this study simulated the abnormal situations of actual modules and applied the binary search algorithm for maximum power point tracking to detect malfunctions of the PV module arrays.