Significant advancements in artificial intelligence (AI) have transformed clinical decision-making, particularly in disease detection and management. Endometriosis, a chronic and often debilitating gynecological disorder, affects a substantial proportion of reproductive-age women and is associated with pelvic pain, infertility, and a reduced quality of life. Despite its high prevalence, non-invasive and accurate diagnostic methods remain limited, frequently resulting in delayed or missed diagnoses. In this study, a novel diagnostic framework was developed by integrating deep learning (DL) with explainable artificial intelligence (XAI) to address existing limitations in the early and non-invasive detection of endometriosis. Abdominopelvic magnetic resonance imaging (MRI) data were obtained from the Crestview Radiology Center in Victoria Island, Lagos State. Preprocessing procedures, including Digital Imaging and Communications in Medicine (DICOM)-to-PNG conversion, image resizing, and intensity normalization, were applied to standardize the imaging data. A U-Net architecture enhanced with a dual attention mechanism was employed for lesion segmentation, while Gradient-weighted Class Activation Mapping (Grad-CAM) was incorporated to visualize and interpret the model’s decision-making process. Ethical considerations, including informed patient consent, fairness in algorithmic decision-making, and mitigation of data bias, were rigorously addressed throughout the model development pipeline. The proposed system demonstrated the potential to improve diagnostic accuracy, reduce diagnostic latency, and enhance clinician trust by offering transparent and interpretable predictions. Furthermore, the integration of XAI is anticipated to promote greater clinical adoption and reliability of AI-assisted diagnostic systems in gynecology. This work contributes to the advancement of non-invasive diagnostic tools and reinforces the role of interpretable DL in the broader context of precision medicine and women's health.