Fogo volcano belongs to the Cape Verde Archipelago, and it is one of the most active volcanoes in the Atlantic Ocean, which most recent eruption occurred from November 2014 to February 2015. We analyzed ambient seismic noise recordings of three different networks deployed in the island, totalizing 14 seismic stations, to derive a crustal 3D shear-wave crustal velocity model of the volcano. Through the phase cross-correlation technique followed by a time-domain phase weighted stack, we were able to measure Rayleigh wave group-velocity dispersion measurements in the period range from 1.0 to 10 s. These dispersion measurements were used to invert for 2D group velocity maps at selected periods, and then inverted to produce a 3D shear-wave velocity model of the island. The tomographic model shows three velocity domains. First, an asymmetric upper layer, above 5–6 km of depth, with lower velocities concentrated in the northeastern sector of the island and a clear higher-velocity horizontal body at 3–4 km of depth in the southwestern sector of the island; the spatial correlation between these two velocity zones and the Galinheiros normal fault suggests a genetic link between the high velocities and long-term surface deformation, which we related to sill intrusions between 3 and 4.5 km depth, beneath the southwestern sector of the island. Second, a marked higher-velocity horizontal layer in between 5 and 6 km and 8–9 km, interpreted as the seismic expression of pervasive sill and laccolith intrusions, now cooled, beneath the volcanic edifice and within the underlying oceanic crust. Third, a lower velocity layer below 8–9 km of depth, more pronounced beneath the northeastern sector, which could be explained by a hotter and possibly melt-rich zone beneath the volcano or a significantly altered/serpentinized crust. Finally, our study also confirms that Fogo lacks any sizable magma chambers (ancient or recent) within the volcanic edifice, in agreement with other geophysical and petrological studies. These observations demonstrate that 3D-ambient noise Rayleigh wave tomography is a powerful tool to image the crustal and upper mantle structure beneath volcanic islands, as shown here for Fogo volcano.