Geothermal resources are frequently associated with silicic calderas which show evidence of geologically-recent activity. Hence development of geothermal sites requires both an understanding of the hydrothermal system of these volcanoes, as well as the deeper magmatic processes which drive them. Here we use shear wave splitting to investigate the hydrothermal system at the silicic peralkaline volcano Aluto in the Main Ethiopian Rift, which has experienced repeated uplift and subsidence since at least 2004. We make over 370 robust observations of splitting, showing that anisotropy is confined mainly to the top ∼3 km of the volcanic edifice. We find up to 10% shear wave anisotropy (SWA) is present with a maximum centred at the geothermal reservoir. Fast shear wave orientations away from the reservoir align NNE–SSW, parallel to the present-day minimum compressive stress. Orientations on the edifice, however, are rotated NE–SW in a manner we predict from field observations of faults at the surface, providing fluid pressures are sufficient to hold two fracture sets open. These fracture sets may be due to the repeated deformation experienced at Aluto and initiated in caldera formation. We therefore attribute the observed anisotropy to aligned cracks held open by over-pressurised gas-rich fluids within and above the reservoir. This study demonstrates that shear wave splitting can be used to map the extent and style of fracturing in volcanic hydrothermal systems. It also lends support to the hypothesis that deformation at Aluto arises from variations of fluid pressures in the hydrothermal system. These constraints will be crucial for future characterisation of other volcanic and geothermal systems, in rift systems and elsewhere.