Oral Squamous Cell Carcinoma is characterized by significant mortality and morbidity. Dental professionals can play an important role in its early detection, thanks to the availability of embedded smart cameras for oral photos and remote screening supported by Deep Learning (DL). Despite the promising results of DL for automated detection and classification of oral lesions, its effectiveness is based on a clearly defined protocol, on the explainability of results, and on periodic cases collection. This paper proposes a novel method, combining DL and Case-Based Reasoning (CBR), to allow the post-hoc explanation of the system answer. The method uses explainability tools organized in a protocol defined in the Business Process Model and Notation (BPMN) to allow its experimental validation. A redesign of the Faster-R-CNN Feature Pyramid Networks (FPN) + DL architecture is also proposed for lesions detection and classification, fine-tuned on 160 cases belonging to three classes of oral ulcers. The DL system achieves state-of-the-art performance, i.e., 83% detection and 92% classification rate (98% for neoplastic vs. non-neoplastic binary classification). A preliminary experimentation of the protocol involved both resident and specialized doctors over selected difficult cases. The system and cases have been publicly released to foster collaboration between research centers.