The frequency characteristics of the resting-state BOLD fMRI (rs-fMRI) signal are of increasing scientific interest, as we discover more frequency-specific biological interpretations. In this work, we use variational mode decomposition (VMD) to precisely decompose the rs-fMRI time series into its intrinsic mode functions (IMFs) in a data-driven manner. The accuracy of the VMD decomposition of constituent IMFs is verified through simulations, with higher reconstruction accuracy and much-reduced mode mixing relative to previous methods. Furthermore, we examine the relative contribution of the VMD-derived modes (frequencies) to the rs-fMRI signal as well as functional connectivity measurements. Our primary findings are: (1) The rs-fMRI signal within the 0.01–0.25 Hz range can be consistently characterized by four intrinsic frequency clusters, centered at 0.028 Hz (IMF4), 0.080 Hz (IMF3), 0.15 Hz (IMF2) and 0.22 Hz (IMF1); (2) these frequency clusters were highly reproducible, and independent of rs-fMRI data sampling rate; (3) not all frequencies were associated with equivalent network topology, in contrast to previous findings. In fact, while IMF4 is most likely associated with physiological fluctuations due to respiration and pulse, IMF3 is most likely associated with metabolic processes, and IMF2 with vasomotor activity. Both IMF3 and IMF4 could produce the brain-network topology typically observed in fMRI, whereas IMF1 and IMF2 could not. These findings provide initial evidence of feasibility in decomposing the rs-fMRI signal into its intrinsic oscillatory frequencies in a reproducible manner.