Dental caries is the most prevalent chronic condition worldwide. Early detection can significantly improve treatment outcomes and reduce the need for invasive procedures. Recently, near-infrared transillumination (TI) imaging has been shown to be effective for the detection of early stage lesions. In this work, we present a deep learning model for the automated detection and localization of dental lesions in TI images. Our method is based on a convolutional neural network (CNN) trained on a semantic segmentation task. We use various strategies to mitigate issues related to training data scarcity, class imbalance, and overfitting. With only 185 training samples, our model achieved an overall mean intersection-over-union (IOU) score of 72.7% on a 5-class segmentation task and specifically an IOU score of 49.5% and 49.0% for proximal and occlusal carious lesions, respectively. In addition, we constructed a simplified task, in which regions of interest were evaluated for the binary presence or absence of carious lesions. For this task, our model achieved an area under the receiver operating characteristic curve of 83.6% and 85.6% for occlusal and proximal lesions, respectively. Our work demonstrates that a deep learning approach for the analysis of dental images holds promise for increasing the speed and accuracy of caries detection, supporting the diagnoses of dental practitioners, and improving patient outcomes.