Uncertainty quantification is critical for ensuring the safety of deep learning-enabled health diagnostics, as it helps the model account for unknown factors and reduces the risk of misdiagnosis. However, existing uncertainty quantification studies often overlook the significant issue of class imbalance, which is common in medical data. In this paper, we propose a class-balanced evidential deep learning framework to achieve fair and reliable uncertainty estimates for health diagnostic models. This framework advances the state-of-the-art uncertainty quantification method of evidential deep learning with two novel mechanisms to address the challenges posed by class imbalance. Specifically, we introduce a pooling loss that enables the model to learn less biased evidence among classes and a learnable prior to regularize the posterior distribution that accounts for the quality of uncertainty estimates. Extensive experiments using benchmark data with varying degrees of imbalance and various naturally imbalanced health data demonstrate the effectiveness and superiority of our method. Our work pushes the envelope of uncertainty quantification from theoretical studies to realistic healthcare application scenarios. By enhancing uncertainty estimation for class-imbalanced data, we contribute to the development of more reliable and practical deep learning-enabled health diagnostic systems1.