Oral Squamous Cell Carcinoma (OSCC) is a common type of cancer of the oral epithelium. Despite their high impact on mortality, sufficient screening methods for early diagnosis of OSCC often lack accuracy and thus OSCCs are mostly diagnosed at a late stage. Early detection and accurate outline estimation of OSCCs would lead to a better curative outcome and a reduction in recurrence rates after surgical treatment. Confocal Laser Endomicroscopy (CLE) records sub-surface micro-anatomical images for in vivo cell structure analysis. Recent CLE studies showed great prospects for a reliable, real-time ultrastructural imaging of OSCC in situ. We present and evaluate a novel automatic approach for OSCC diagnosis using deep learning technologies on CLE images. The method is compared against textural feature-based machine learning approaches that represent the current state of the art. For this work, CLE image sequences (7894 images) from patients diagnosed with OSCC were obtained from 4 specific locations in the oral cavity, including the OSCC lesion. The present approach is found to outperform the state of the art in CLE image recognition with an area under the curve (AUC) of 0.96 and a mean accuracy of 88.3% (sensitivity 86.6%, specificity 90%).