Measuring pupillary response is a prevalent technique to evaluate mental states. It is indispensable to conduct a correction procedure for the pupillary baseline to get a meaningful conclusion from the pupillary response. However, the relationship between pupillary baseline and subsequent stimulus-evoked pupillary response varies among studies. In this study, we used the subtractive and proportional baseline corrections to analyze the results. Furthermore, we manipulated the pupillary baseline through mental effort or luminance in the baseline period and investigated whether the subsequent stimulus-evoked pupillary responses were affected. We found that the mental effort-evoked pupillary response was attenuated with a larger pupillary baseline manipulated by a higher mental effort, whereas it was unaffected with the baseline manipulated by luminance. Also, the luminance-evoked pupillary response was attenuated with a smaller pupillary baseline manipulated by a brighter disk, whereas it was unaffected with the baseline manipulated by mental effort. The results could be obtained from subtractive and proportional baseline corrections. Our results suggest that mental effort manipulated pupillary baseline interacts with the subsequent mental effort elicited pupillary response, but not with the luminance elicited pupillary response; the luminance manipulated pupillary baseline interacts with the subsequent luminance elicited pupillary response, but not with the mental effort elicited pupillary response. It is important to consider the ways of controlling the pupillary baseline and subsequent pupillary response simultaneously.