In uncertain environments, we balance exploitation and exploration: we generally exploit rewarding opportunities, but sometimes explore uncertain alternatives that could be even better. Exploration is associated with a sudden disorganization of neuronal activity patterns in the prefrontal cortex, which could be a powerful way to promote discovery and learning. Although the mechanisms behind this disorganization remain unknown, one possibility is pupil-linked neuromodulatory systems. However, it is not clear whether pupil size predicts the neural signatures of exploration, much less the sudden transitions that occur at the onset of exploration. Here, we simultaneously measured pupil size and neuronal activity in the prefrontal cortex while two rhesus macaques made decisions in a dynamic environment that encouraged both exploration and exploitation. Consistent with our expectations from previous studies, we found that pupil size was larger during exploration than exploitation. Pupil size also predicted disorganized patterns of prefrontal activity in both single neurons and the population. This was true even within periods of exploitation. The pupil also exhibited surprising trial-by-trial dynamics: it grew larger across trials before exploration, then abruptly decreased to below-baseline levels. Because pupil size began decreasing immediately after the first explore trial, pupil-linked mechanisms may anticipate the start of exploration, without being sustained throughout periods of exploration. Indeed, before the onset of exploration, we observed a general slowing of both response time and neural activity, consistent with the idea that the onset of exploration represents a critical “tipping point” in prefrontal dynamics. Pupil size, in turn, predicted this slowing. In sum, we found that pupil size tracked both exploratory behavior and its neural correlates, supporting models that connect pupil-linked mechanisms in these phenomena. However, the trial-by-trial dynamics of these effects specifically implicate pupil-linked mechanisms in the critical transition at the onset of exploration, rather than in sustaining exploration over time.