Diagnosing clinically unclear basal cell carcinomas (BCCs) can be challenging. Line-field confocal optical coherence tomography (LC-OCT) is able to display morphological features of BCC subtypes with good histological correlation. The aim of this study was to investigate the accuracy of LC-OCT in diagnosing clinically unsure cases of BCC compared to dermoscopy alone and in distinguishing between superficial BCCs and other BCC subtypes. Moreover, we addressed pitfalls in false positive cases. We prospectively enrolled 182 lesions of 154 patients, referred to our department to confirm or to rule out the diagnosis of BCC. Dermoscopy and LC-OCT images were evaluated by two experts independently. Image quality, LC-OCT patterns and criteria, diagnosis, BCC subtype, and diagnostic confidence were assessed. Sensitivity and specificity of additional LC-OCT were compared to dermoscopy alone for identifying BCC in clinically unclear lesions. In addition, key LC-OCT features to distinguish between BCCs and non-BCCs and to differentiate superficial BCCs from other BCC subtypes were determined by linear regressions. Diagnostic confidence was rated as “high” in only 48% of the lesions with dermoscopy alone compared to 70% with LC-OCT. LC-OCT showed a high sensitivity (98%) and specificity (80%) compared to histology, and these were even higher (100% sensitivity and 97% specificity) in the subgroup of lesions with high diagnostic confidence. Interobserver agreement was nearly perfect (95%). The combination of dermoscopy and LC-OCT reached a sensitivity of 100% and specificity of 81.2% in all cases and increased to sensitivity of 100% and specificity of 94.9% in cases with a high diagnostic confidence. The performance of LC-OCT was influenced by the image quality but not by the anatomical location of the lesion. The most specific morphological LC-OCT criteria in BCCs compared to non-BCCs were: less defined dermoepidermal junction (DEJ), hyporeflective tumor lobules, and dark rim. The most relevant features of the subgroup of superficial BCCs (sBCCs) were: string of pearls pattern and absence of epidermal thinning. Our diagnostic confidence, sensitivity, and specificity in detecting BCCs in the context of clinically equivocal lesions significantly improved using LC-OCT in comparison to dermoscopy only. Operator training for image acquisition is fundamental to achieve the best results. Not only the differential diagnosis of BCC, but also BCC subtyping can be performed at bedside with LC-OCT.