Pupil dilation, an indicator of arousal that is generally regarded as unspecific, amongst others reflects decision formation and reveals choice. Employing letter selection in a Go/NoGo task, we show that choice can robustly be predicted by the pupillary signal, even under the presence of strong interfering factors such as changes in brightness or motor execution. In addition, a larger difference in pupil dilation between target and distractor conditions for NoGo compared to Go was demonstrated, underlining the particular appropriateness of the paradigm for decision research. Incorporating microsaccades, a variable that is suggested to covary with pupil diameter, we show that decision formation can only be observed in pupil diameter. However, microsaccade rate and pupil size covaried for motor execution and both reflected choice after key press with smaller effect size for microsaccade rate. We argue that combining pupil dilation and microsaccade rate may help dissociating decision-related changes in pupil diameter from interfering factors. Considering the interlinked main neural correlates of pupil dilation and microsaccade generation, these findings point to a selective role of locus coeruleus compared to superior colliculus in decision formation.