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Epidermolysis bullosa acquisita (EBA) represents a big challenge as a rare skin disorder, with no established markers for early detection for patients. Moreover, as a rare disease, it is extremely difficult to acquire good number of patient sample to diagnose accurately with high confidence. EBA has many biomarkers very similar to other bullosa diseases and needs specific clinical expertise to detect it using immunofluorescence microscopy. In this study, we introduce a deep learningbased method, EBAnet, that leveraged Convolutional Neural Network (CNN) based model for the detection of EBA based on Direct immunofluorescence (DIF) microscopy image. The proposed EfficientNet-based model achieved 97.3% sensitivity, 96.1% precision, and 96.7% accuracy in distinguishing EBA from other class and outperformed the existing model for the same purpose. GradCAM based class activation map also highlighted the important region of the DIF images that was focused by the proposed model leveraging the explainability of the model. We believe, EBAnet will add value in the early and accurate detection of EBA, addressing a critical need in clinical practice.