This study aimed to identify the anterior segment high-resolution optical coherence tomography (HR-OCT) and HR-OCT angiography (HR-OCTA) features suggestive of limbal stem cell deficiency (LSCD) as confirmed by both impression cytology (IC) and in vivo confocal microscopy (IVCM). This was a single-centre prospective cross-sectional study including 24 eyes of 22 patients with clinical suspicion of LSCD based on peripheral superficial corneal vascularisation and scarring. On IC and IVCM, performed and interpreted by blinded observers, 12 eyes each were diagnosed with and without LSCD. Additionally, 10 eyes of 5 healthy volunteers with no ocular pathology were also imaged. The 136 HR-OCT/A images of these 34 eyes were analysed with respect to 12 imaging parameters; the parameters most suggestive of LSCD were identified and the sensitivity and specificity were calculated. In the LSCD group, the most common aetiology was ocular chemical burns (83%), whereas in the non-LSCD group, the most common aetiology was viral keratitis (67%). Multiple logistic regression analysis revealed that mean epithelial reflectivity, mean stromal reflectivity, and mean superficial vascular density were the parameters that were diagnostic of LSCD on HR-OCT/A (p < 0.0001). A ratio of the mean epithelial reflectivity to stromal reflectivity of >1.29 corresponded with a high sensitivity (91.7%) and specificity (98.75%); while a mean superficial vascular density score of >0.38 corresponded with a sensitivity of 97.9% and specificity of 73.8%. In conclusion, HR-OCT/A as a non-invasive imaging modality could prove to be a useful tool for confirming the diagnosis of LSCD, with potential clinical and research applications.