Isolated rapid eye movement sleep behavior disorder (iRBD) is a sleep disorder characterized by dream enactment behavior without any neurological disease and is frequently accompanied by cognitive dysfunction. The purpose of this study was to reveal the spatiotemporal characteristics of abnormal cortical activities underlying cognitive dysfunction in patients with iRBD based on an explainable machine learning approach. A convolutional neural network (CNN) was trained to discriminate the cortical activities of patients with iRBD and normal controls based on three-dimensional input data representing spatiotemporal cortical activities during an attention task. The input nodes critical for classification were determined to reveal the spatiotemporal characteristics of the cortical activities that were most relevant to cognitive impairment in iRBD. The trained classifiers showed high classification accuracy, while the identified critical input nodes were in line with preliminary knowledge of cortical dysfunction associated with iRBD in terms of both spatial location and temporal epoch for relevant cortical information processing for visuospatial attention tasks.