Many everyday choices are based on personal, subjective preferences. When choosing between two options, we often feel conflicted, especially when trading off costs and benefits occurring at different times (e.g., saving for later versus spending now). Although previous work has investigated the neurophysiological basis of conflict during inhibitory control tasks, less is known about subjective conflict resulting from competing subjective preferences. In this pre-registered study, we investigated subjective conflict during intertemporal choice, whereby participants chose between smaller immediate versus larger delayed rewards (e.g., $15 today vs. $22 in 30 days). We used economic modeling to parametrically vary eleven different levels of conflict, and recorded EEG data and pupil dilation. Midfrontal theta power, derived from EEG, correlated with pupil responses, and our results suggest that these signals track different gradations of subjective conflict. Unexpectedly, both signals were also maximally enhanced when decisions were surprisingly easy. Therefore, these signals may track events requiring increased attention and adaptive shifts in behavioral responses, with subjective conflict being only one type of such event. Our results suggest that the neural systems underlying midfrontal theta and pupil responses interact when weighing costs and benefits during intertemporal choice. Thus, understanding these interactions might elucidate how individuals resolve self-control conflicts.