Deep neural network (DNN) classifiers are often overconfident, producing miscalibrated class probabilities. In high-risk applications like healthcare, practitioners require fully calibrated probability predictions for decision-making. That is, conditioned on the prediction vector, every class’ probability should be close to the predicted value. Most existing calibration methods either lack theoretical guarantees for producing calibrated outputs, reduce classification accuracy in the process, or only calibrate the predicted class. This paper proposes a new Kernel-based calibration method called KCal. Unlike existing calibration procedures, KCal does not operate directly on the logits or softmax outputs of the DNN. Instead, KCal learns a metric space on the penultimate-layer latent embedding and generates predictions using kernel density estimates on a calibration set. We first analyze KCal theoretically, showing that it enjoys a provable full calibration guarantee. Then, through extensive experiments across a variety of datasets, we show that KCal consistently outperforms baselines as measured by the calibration error and by proper scoring rules like the Brier Score.