Anti‐atheist prejudice is pervasive worldwide. Past research indicates that this is driven by perceptions of atheist immorality, yet such perceptions have not been explored in detail. Using Moral Foundations Theory and samples of U.S. Christians, we investigated whether anti‐atheist prejudice is explained by atheists' perceived adherence to certain foundational moral values more than others. Study 1 participants completed measures of moral value endorsements from the perspective of a typical atheist. Study 2 participants read that either atheists or people in general strongly endorse one of five moral foundations. Anti‐atheist prejudice was consistently explained best by perceived atheist concern for values of caring/compassion rather than fairness/justice, loyalty, deferential respect, or purity/decency. Findings suggest that efforts to reduce anti‐atheist prejudice should emphasize atheists' capacity for kindness and caring.