The Tuareg Shield, to which Hoggar (southern Algeria) belongs, has a swell-shaped morphology of lithospheric scale of ~1000 km in diameter linked to Cenozoic volcanism occurring in several regions, including Atakor, the center of the swell, which reaches nearly 3000 m in altitude. The lack of high-resolution geophysical data for constraining its deep structure is at the origin of a controversy about its innermost nature and about the origin of the Cenozoic volcanism. During the course of this study, magnetotelluric (MT) broadband data were collected at 18 sites forming a northeast-southwest profile 170 km long within the Atakor region. The electrical resistivity model obtained by inverting the magnetotelluric data reveals lithospheric structure down to a depth of ~100 km. From this depth to the surface, the model does not show any regional anomaly that may result from a metasomatized lithosphere or from an asthenospheric upwelling, including a mantle plume. MT data reveal rather a lithosphere affected by a set of rather thin subvertical conductors that can be attributed to the electrical signature of some known shear zones resulting from the Pan-African evolution of the LATEA metacraton, which globally corresponds to the uplifted Central Hoggar swell. The main anomaly is deeply rooted in the lithosphere and underlies the Atakor-Manzaz volcanic districts. As a whole, MT data are therefore properly integrated within the hypothesis of the reactivation of shear zones due the intraplate deformation related to the collision between Africa and Europe since the Eocene, applied onto the metacratonic region.