Rapid eye movement (REM) sleep has been frequently associated with dreaming. However, mounting evidence obtained from behavioral, pharmacological, and brain imaging studies suggests that REM sleep is not indicative of the dream report and may originate from diverse neural substrates in brain functionality. The aim of the current study was to investigate the functional systems associated with inter-individual differences in dream recall and REM sleep through assessments of the resting-state functional connectivity. We collected resting-state functional magnetic resonance imaging (fMRI) data for functional connectivity evaluations from 43 healthy adult volunteers (23 men) before and after sleep. For assessment of the dream recall frequency, a 2-week sleep diary was maintained by all volunteers. In addition, whole-night polysomnography was performed for measuring the REM sleep percentage. Voxel-wise correlation analyses of 12 functional connectivity networks of interest with the dream recall frequency and REM sleep percentage were conducted using general linear model analysis. Both the dream recall frequency and REM sleep percentage showed negative associations with multiple brain functional networks. However, the dream recall frequency was mainly related to functional connectivity within the lateral visual network and thalamus, whereas the REM sleep percentage was mainly associated with connectivity within the frontoparietal networks and cerebellum. In addition, the dream recall frequency showed stronger coupling with the lateral visual network connectivity at night, whereas the coupling between the REM sleep percentage and cerebellum was higher in the morning. This indicated a significant time of day effect. Our results provide neuroimaging evidence that the functional system associated with the dream recall frequency is different from that associated with the REM sleep percentage.