Involuntary microsaccades and voluntary saccades reflect human brain activities during attention and cognitive tasks. Our eye movements can also betray our emotional state. However, the effects of attention to emotion on microsaccadic activity remain unknown. The present study was conducted in healthy volunteers to investigate the effects of devoting attention to exogenous emotional stimuli on microsaccadic response, with change in pupil size as an index of sympathetic nervous system activity. Event-related responses to unpleasant images significantly inhibited the rate of microsaccade appearance and altered pupil size (Experiment 1). Additionally, microsaccadic responses to covert orienting of attention to emotional stimuli appeared significantly in the anti-direction to a target, with a fast reaction time (Experiment 2). Therefore, we concluded that attentional shifts induced by exogenous emotional stimuli can modulate microsaccadic activities. Future studies of the interaction between miniature eye movements and emotion may be beneficial in the assessment of pathophysiological responses in mental disorders.