Mind-wandering (MW) refers to the shift of attention away from an ongoing task and/or external environment towards mental contents (e.g., memories, prospective thoughts) unrelated to the task. Physiological measures (e.g., pupil size, EEG, and fMRI) have often been acquired as objective markers for MW states, which has greatly helped their study as well as triangulation with other measures. Pupillometry in particular has been used as a covert biomarker of MW because it is reliably modulated by several distinct processes spanning arousal, emotion, and attention, and it signals attentional lapses. Yet, coupling MW and the measurement of pupil size has led to seemingly contrasting results. We argue that, common to the studies reviewed here, one reason is resolving to the measurement of tonic pupil size, which reflects low-frequency, slow changes in one’s physiological state, and thus implicitly assumes that MW is a static, long-lasting process. We then additionally focus on three major axes of variability in the reviewed studies: (i) the definition and measurement of MW; (ii) the impact of contextual aspects, such as task demands and individual arousal levels; (iii) the identification and tracking of MW in combination with pupillary measures. We provide an overview of these differences and put forward recommendations for using physiological measures—including, but not limited to, pupil size—in MW research effectively. In conclusion, pupillometry can be a very informative tool for MW research, provided that it is used with the due methodological caution.