Stridor is a rare but important non-motor symptom that can support the diagnosis and prediction of worse prognosis in multiple system atrophy. Recording sounds generated during sleep by video-polysomnography is recommended for detecting stridor, but the analysis is labor intensive and time consuming. A method for automatic stridor detection should be developed using technologies such as artificial intelligence (AI) or machine learning. However, the rarity of stridor hinders the collection of sufficient data from diverse patients. Therefore, an AI method with high diagnostic performance should be devised to address this limitation. We propose an AI method for detecting patients with stridor by combining audio splitting and reintegration with few-shot learning for diagnosis. We used video-polysomnography data from patients with stridor (19 patients with multiple system atrophy) and without stridor (28 patients with parkinsonism and 18 patients with sleep disorders). To the best of our knowledge, this is the first study to propose a method for stridor detection and attempt the validation of few-shot learning to process medical audio signals. Even with a small training set, a substantial improvement was achieved for stridor detection, confirming the clinical utility of our method compared with similar developments. The proposed method achieved a detection accuracy above 96% using data from only eight patients with stridor for training. Performance improvements of 4%–13% were achieved compared with a state-of-the-art AI baseline. Moreover, our method determined whether a patient had stridor and performed real-time localization of the corresponding audio patches, thus providing physicians with support for interpreting and efficiently employing the results of this method.