Abstract We propose a generic framework to calibrate accuracy and confidence of a prediction in deep neural networks through stochastic inferences. We interpret stochastic regularization using a Bayesian model, and analyze the relation between predictive uncertainty of networks and variance of the prediction scores obtained by stochastic inferences for a single example. Our empirical study shows that the accuracy and the score of a prediction are highly correlated with the variance of multiple stochastic inferences given by stochastic depth or dropout. Motivated by this observation, we design a novel variance-weighted confidence-integrated loss function that is composed of two cross-entropy loss terms with respect to ground-truth and uniform distribution, which are balanced by variance of stochastic prediction scores. The proposed loss function enables us to learn deep neural networks that predict confidence calibrated scores using a single inference. Our algorithm presents outstanding confidence calibration performance and improves classification accuracy when combined with two popular stochastic regularization techniques—stochastic depth and dropout—in multiple models and datasets; it alleviates overconfidence issue in deep neural networks significantly by training networks to achieve prediction accuracy proportional to confidence of prediction.