Introduction: Cholangiocarcinoma (CCA) is a highly lethal malignancy originating in the bile ducts, often diagnosed late with poor prognosis. Differentiating benign from malignant biliary tumors remains challenging, necessitating advanced diagnostic techniques. Objective: This study aims to enhance the diagnostic accuracy of endoscopic ultrasound (EUS) for distal cholangiocarcinoma (dCCA) using advanced convolutional neural networks (CCNs) for the classification and segmentation of EUS images, specifically targeting dCCAs, the pancreas, and the bile duct. Materials and Methods: In this retrospective study, EUS images from patients diagnosed with dCCA via biopsy and an EUS-identified bile duct tumor were evaluated. A custom CNN was developed for classification, trained on 156 EUS images. To enhance the model’s robustness, image augmentation techniques were applied, generating a total of 1248 images. For tumor and organ segmentation, the DeepLabv3+ network with ResNet50 architecture was utilized, employing Tversky loss to manage unbalanced classes. Performance evaluation included metrics such as accuracy, sensitivity, specificity, and Intersection over Union (IoU). These methods were implemented in collaboration with the ADAPTED Research Group at the Technical University of Cluj-Napoca. Results: The classification model achieved a high accuracy of 97.82%, with precision and specificity both at 100% and sensitivity at 94.44%. The segmentation models for the pancreas and bile duct demonstrated global accuracies of 84% and 90%, respectively, with robust IoU scores indicating good overlap between predicted and actual contours. The application performed better than the UNet model, particularly in generalization and boundary delineation. Conclusions: This study demonstrates the significant potential of AI in EUS imaging for dCCA, presenting a robust tool that enhances diagnostic accuracy and efficiency. The developed MATLAB application serves as a valuable aid for medical professionals, facilitating informed decision-making and improving patient outcomes in the diagnosis of cholangiocarcinoma and related pathologies.