Our experience of reasoning is replete with conflict. People phenomenologically vacillate between options when confronted with challenging decisions. Existing experimental designs typically measure a summary of the experience of the conflict experienced throughout the choice process for any individual choice or even between multiple observers for a choice. We propose a new method for measuring vacillations in reasoning during the time-course of individual choices, utilizing them as a fine-grained indicator of cognitive conflict. Our experimental paradigm allows participants to report the alternative they were considering while deliberating. Through 3 experiments, we demonstrate that our measure correlates with existing summary judgments of conflict and confidence in moral and logical reasoning problems. The pattern of deliberation revealed by these vacillations produces new constraints for theoretical models of moral and syllogistic reasoning.