When testing primates with cognitive tasks, it is usually not considered that subjects differ markedly in terms of emotional reactivity toward the experimenter, which potentially affects a subject’s cognitive performance. We addressed this issue in common marmosets (Callithrix jacchus), a monkey species in which males tend to show stronger emotional reactivity in testing situations, whereas females have been reported to outperform males in cognitive tasks. In a two-phase experiment, we first quantified the emotional reactivity of 14 subjects toward four different experimenters performing a standardized behavioral action sequence and then assessed whether and how it affected the subjects’ participation and performance in a subsequent object permanence task. A test session was terminated if a subject refused to make a choice in four consecutive trials. Highly emotionally aroused individuals, particularly males, were less likely to participate in the cognitive task and completed fewer trials. However, whenever they did participate and were attentive to the task, their performance was not affected. Our results suggest that differences in emotional reactivity toward an experimenter have no major impact on cognitive performance if strict criteria are applied on when to abandon a test session and if performance is corrected for attention to the test procedure. Furthermore, they suggest that the reported sex differences in cognitive performance in marmosets may be owing to motivational and attentional factors, rather than a difference in cognitive ability per se.