Gastrointestinal diseases such as gastroesophageal reflux disease (GERD) and polyps remain prevalent and challenging to diagnose accurately due to overlapping visual features and inconsistent endoscopic image quality. In this study, we investigate the application of transformer-based deep learning models—Vision Transformer (ViT), Swin Transformer, and a novel Ensemble Transformer model—for classifying four categories: GERD, GERD Normal, Polyp, and Polyp Normal from endoscopic images. The dataset was curated and collected in collaboration with Zainul Haque Sikder Women's Medical College & Hospital, ensuring high-quality clinical annotations. All models were evaluated using precision, recall, F1 score, and overall classification accuracy. Our proposed Ensemble Transformer model, which fuses the outputs of ViT and Swin Transformer, achieved superior performance by delivering well-balanced F1 scores across all classes, reducing misclassification, and improving robustness with an overall accuracy of 87%. Furthermore, we incorporated explainable AI (XAI) techniques such as Grad-CAM and Grad-CAM++ to generate visual explanations of the model’s predictions, enhancing interpretability for clinical validation. This work demonstrates the potential of integrating global and local attention mechanisms along with XAI in building reliable, real-time, AI-assisted diagnostic support systems for gastrointestinal disorders, particularly in resource-limited healthcare settings.