Major advances in resting-state functional magnetic resonance imaging (fMRI) techniques in the last two decades have provided a tool to better understand the functional organization of the brain both in health and illness. Despite such developments, characterizing regulation and cerebral representation of mind wandering, which occurs unavoidably during resting-state fMRI scans and may induce variability of the acquired data, remains a work in progress. Here, we demonstrate that a decrease or decoupling in functional connectivity involving the caudate nucleus, insula, medial prefrontal cortex and other domain-specific regions was associated with more sustained mind wandering in particular thought domains during resting-state fMRI. Importantly, our findings suggest that temporal and between-subject variations in functional connectivity of above-mentioned regions might be linked with the continuity of mind wandering. Our study not only provides a preliminary framework for characterizing the maintenance and cerebral representation of different types of mind wandering, but also highlights the importance of taking mind wandering into consideration when studying brain organization with resting-state fMRI in the future. Over the past two decades, resting-state functional connectivity measured by functional magnetic resonance imaging (fMRI) has played an essential role in understanding brain functional networks in healthy and patient populations 1–5. Resting-state functional connectivity is measured by the temporal co-activation level of spontaneous fMRI signals between spatially distinct brain regions in the absence of a perceptual or behavioral task 6. Although the participants are not engaged in any particular task, there is increasing evidence that spontaneous thoughts (known as mind wandering, daydreaming, self-generated mental activity or task-unrelated thought) that are minimally constrained by external perception emerge during fMRI scans and may potentially affect resting-state fMRI data 7,8. Mind wandering during resting-state fMRI has been assessed using different approaches. Questionnaires can be administered, following the resting-state fMRI scan, in which participants are asked to report the presence and frequency of spontaneous thoughts across various domains. Resting-state fMRI studies have employed several types of retrospective measures to assess spontaneous thoughts: Amsterdam Resting-State Questionnaire (ARSQ) 9 , New York Cognition Questionnaire (NYC-Q) 10–12 , and Resting-State Questionnaire (ReSQ) 13,14. Alternatively, mind-wandering has been assessed using experience or thought sampling in conjunction with resting-state fMRI scanning 15–20. While regions within the default mode network