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How does rationality shape cooperation in strategic settings? We study this question in a laboratory experiment that links individual rationality, measured by consistency with the generalized axiom of revealed preference, to behaviour in an indefinitely repeated Prisoner’s Dilemma. Participants are grouped by pre-measured rationality before interacting repeatedly. We find that higher rationality substantially increases cooperation and payoffs. This effect operates through a novel mechanism: more rational individuals make fewer implementation errors when executing their intended strategies, thereby sustaining cooperative outcomes. By contrast, higher cognitive ability also promotes cooperation and higher payoffs, but through a distinct channel—reducing strategic errors in responding optimally to others’ actions. Our results provide the first experimental evidence linking rationality to cooperation via decision-making errors, and clarify the distinct roles of rationality and intelligence in shaping strategic behaviour. Together, the findings offer a unified account of how cognitive constraints affect cooperation in repeated games.