Functional ultrasound (fUS) imaging has recently allowed 3D functional imaging in awake mice using motorized linear or matrix arrays (Brunner et al., 2020; Bertolo et al., 2021). However, the tradeoff between the field of view and temporal resolution introduced by motorized scanning hinders acquiring whole-brain resting state Functional Connectivity (rsFC), whereas the limited sensitivity of matrix arrays prevents transcranial imaging in mice. Here we propose a new hybrid approach dedicated to 3D rsFC in the whole mouse brain with intact skull.A newly developed 15 MHz multiarray probe (IcoPrime 4D MultiArray, pitch 110 µm, Iconeus), allowing the simultaneous acquisition of four power Doppler slices separated by 2.1 mm, was mounted on a 4-axis motor stage. Fast motorization enabled the continued acquisition of 16 contiguous slices (525 µm step) within 2.4s. To validate this approach, we compared image quality with Row-Column Addressing (RCA) and matrix probes in the same mouse and performed 20-minute rsFC acquisitions in n=6 awake, head-fixed mice.Having demonstrated that our approach provides a better image quality compared to other existing 3D fUS modalities, we evaluated rsFC data with seed-based and ICA. Several long-range FC patterns were identified in both cortical and subcortical brain areas, corresponding to functional networks already described in previous fMRI studies.Together, these results demonstrate that the multi-array probe is a valuable approach for measuring brain-wide hemodynamic activity in mice with an intact skull. Its ability to identify robust resting-state networks paves the way for a better understanding of the mouse brain functional organization.