While deep AUC maximization (DAM) has shown remarkable success on imbalanced medical tasks, e.g., chest X-rays classification and skin lesions classification, it could suffer from severe overfitting when applied to small datasets due to its aggressive nature of pushing prediction scores of positive data away from that of negative data. This paper studies how to improve generalization of DAM by mixup data augmentation- an approach that is widely used for improving generalization of the cross-entropy loss based deep learning methods. However, AUC is defined over positive and negative pairs, which makes it challenging to incorporate mixup data augmentation into DAM algorithms. To tackle thischallenge, we employ the AUC margin loss and incorporate soft labels into the formulation to effectively learn from data generated by mixup augmentation, which is referred to as the AUC-mixup loss. Our experimental results demonstrate the effectiveness of the proposed AUC-mixup methods on imbalanced benchmark and medical image datasets compared to standard DAM training.