We used aeromagnetic and gravity data to investigate the thermal structure beneath the incipient Okavango Rift Zone (ORZ) in northwestern Botswana in order to understand its role in strain localization during rift initiation. We used three‐dimensional (3‐D) inversion of aeromagnetic data to estimate the Curie Point Depth (CPD) and heat flow under the rift and surrounding basement. We also used two‐dimensional (2‐D) power‐density spectrum analysis of gravity data to estimate the Moho depth. Our results reveal shallow CPD values (8–15 km) and high heat flow (60–90 mW m⁻²) beneath a ~60 km wide NE‐trending zone coincident with major rift‐related border faults and the boundary between Proterozoic orogenic belts. This is accompanied by thin crust (<30 km) in the northeastern and southwestern parts of the ORZ. Within the Precambrian basement areas, the CPD values are deeper (16–30 km) and the heat flow estimates are lower (30–50 mW m⁻²), corresponding to thicker crust (~40–50 km). We interpret the thermal structure under the ORZ as due to upward migration of hot mantle fluids through the lithospheric column that utilized the presence of Precambrian lithospheric shear zones as conduits. These fluids weaken the crust, enhancing rift nucleation. Our interpretation is supported by 2‐D forward modeling of gravity data suggesting the presence of a wedge of altered lithospheric mantle centered beneath the ORZ. If our interpretation is correct, it may result in a potential paradigm shift in which strain localization at continental rift initiation could be achieved through fluid‐assisted lithospheric weakening without asthenospheric involvement.