Pupil size reflects a proxy for neural activity associated with global luminance, arousal and cognitive processing. Microsaccades are also modulated by arousal and cognitive processing. Are these effects of arousal and cognitive signals on pupil size and microsaccades coordinated? If so, via what neural mechanisms? We hypothesized that if pupil size and microsaccades are coordinately modulated by these processes, pupil size immediately before microsaccade onset, as an index for ongoing cognitive and arousal processing, should correlate with microsaccade responses during tasks alternating these signals. Here, we examined the relationship between pupil size and microsaccade responses in tasks that included variations in global luminance, arousal and inhibitory control. Higher microsaccade peak velocities correlated with larger pre-microsaccade pupil response related to arousal and inhibitory control signals. In contrast, pupil responses evoked by global luminance signals did not correlate with microsaccade responses. Given the central role of the superior colliculus in microsaccade generation, these results suggest the critical involvement of the superior colliculus to coordinate pupil and microsaccade responses for arousal and inhibitory control modulations, but not for the pupil luminance modulation.