Cooperative behaviors are typically investigated using social dilemmas inserted into scenarios with well-known characteristics. Nonetheless, in real life, group members may be uncertain about what others will decide (social uncertainty) and the characteristics of the dilemma itself (environmental uncertainty). Previous studies have shown that uncertainty reduces the willingness to cooperate. Dual-process approaches to cooperation have given rise to two different views. Some authors argue that deliberation is needed to overrule selfish motives, whereas others argue that intuition favors cooperation. In this work, our goal was to investigate the role of intuitive mental processing on cooperation in a prisoner's dilemma game involving uncertainty. Our results showed that participants cooperated less with their counterparts as the number of rounds progressed, suggesting a learning process and that intuitive mental processing in the first 50 rounds appears to favor cooperation under both deterministic and stochastic conditions. These results may help clarify the literature's mixed effects regarding cognitive processing manipulation on cooperation. Developing a better understanding of these effects may improve strategies in social problems involving cooperation under uncertainty and cognitive constraints.