Is the brain at rest during the so-called resting-state? Ongoing experiences in the resting-state vary in unobserved and uncontrolled ways across time, individuals, and populations. However, the role of self-generated thoughts in resting-state fMRI remains largely unexplored. In this study, we collected real-time self-generated thoughts during resting-state fMRI scans via the think-aloud method (i.e., think-aloud fMRI), which required participants to report whatever they were currently thinking. We first investigated brain activation patterns during a think-aloud condition and found that significantly activated brain areas included all brain regions required for speech, along with a large number of deactivated brain regions. We then calculated the relationship between divergence in thought content and brain activation during think-aloud, and found that divergence in thought content was associated with a large number of brain regions, including those that were significantly activated and deactivated during think-aloud. Finally, we explored the neural representation of self-generated thoughts by performing representational similarity analysis (RSA) at three neural scales: a voxel-wise whole-brain searchlight level; a region-level whole-brain analysis using the Schaefer 400-parcels; a system level using the Yeo seven-network systems and the language subsystems. We found that resting-state self-generated thoughts were distributed across a wide range of brain regions, involving all Yeo seven-network. This study highlights the importance of taking into account ongoing experiences during resting-state fMRI, as well as providing preliminary methodological support for think-aloud fMRI.