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• Development of a fault detection algorithm on aIRT images highlighting its main challenges, shortcomes, and workarounds; • Utilization of an orthomosaic reconstruction software package describing the challenges that the workflow impose for the automatic fault detection algorithms; • Evaluation of the impact of different flight configurations and dataset on the processing time and results; • Application of the proposed framework in real cases, evaluating the challenges imposed by real datasets. As large-scale Photovoltaic (PV) power plants are being expanded in installation number and capacity, aerial infrared thermography (aIRT) has proven to be effective in detecting at different phases of their development, construction and commissioning to operation and maintenance. However, evaluating the aerial imagery over hundreds of hectares fields of PV arrays is very time-consuming and subject to human error. This paper proposes a complete framework for automatically detecting faults in large-scale PV power plants and their physical location inside the plant site. To this end, a Mask-RCNN algorithm is developed and fine-tuned for instance segmentation using a dataset of 93 samples collected in an aIRT flight campaign in Brazil. The results are combined with orthomosaic techniques to create an orthomap of the PV system with the highlighted faults. The proposed method has been tested to automatically detect the faults in two power plants. Several tests were performed to improve the algorithm's accuracy, resulting in high-accuracy results for detecting and localizing hot spots in PV plants and disconnected substrings. The resulting maps could successfully show the location of these faults with high accuracy (10% of false positives). [ABSTRACT FROM AUTHOR]