Wind disturbances are significant phenomena in forest spatial structure and succession dynamics. They cause changes in biodiversity, impact on forest ecosystems at different spatial scales, and have a strong influence on economics and human beings. The reliable recognition and mapping of windthrow areas are of high importance from the perspective of forest management and nature conservation. Recent research in artificial intelligence and computer vision has demonstrated the incredible potential of neural networks in addressing image classification problems. The most efficient algorithms are based on artificial neural networks of nested and complex architecture (e.g., convolutional neural networks (CNNs)), which are usually referred to by a common term—deep learning. Deep learning provides powerful algorithms for the precise segmentation of remote sensing data. We developed an algorithm based on a U-Net-like CNN, which was trained to recognize windthrow areas in Kunashir Island, Russia. We used satellite imagery of very-high spatial resolution (0.5 m/pixel) as source data. We performed a grid search among 216 parameter combinations defining different U-Net-like architectures. The best parameter combination allowed us to achieve an overall accuracy for recognition of windthrow sites of up to 94% for forested landscapes by coniferous and mixed coniferous forests. We found that the false-positive decisions of our algorithm correspond to either seashore logs, which may look similar to fallen tree trunks, or leafless forest stands. While the former can be rectified by applying a forest mask, the latter requires the usage of additional information, which is not always provided by satellite imagery.