Background Severe aortic stenosis (AS) is associated with ischemic stroke independently of atrial fibrillation or other causes. Even after aortic valve replacement (AVR), patients remain affected by a 6% 5‐year stroke rate with knowledge gaps in the underlying pathophysiology. We hypothesize that severe AS is associated with prothrombotic left atrial (LA) flow changes that do not normalize after AVR. Methods Seventy‐seven participants without atrial fibrillation were recruited: 40 with severe AS (median age, 73 years; CHA 2 DS 2 VASc score, 3) and 37 controls with similar risk profile (median age, 71 years; CHA 2 DS 2 VASc score, 3). All underwent baseline cardiac magnetic resonance imaging. Among the 40 patients with AS, 23 (58%) underwent AVR and repeat cardiac magnetic resonance imaging ≈6 months after surgery. Results Compared with controls, patients with severe AS displayed significantly higher left ventricular (LV) mass ( P =0.04), smaller LV volumes ( P =0.01), and reduced global longitudinal strain ( P <0.001). Although LA volume was within the normal range and LA emptying fraction was not different from controls, severe AS was associated with lower LA peak flow velocity (mean, 0.25 versus 0.28 m/s, respectively; P =0.02) and lower LA flow vorticity (mean, 16.6 versus 21.1 radians; P <0.001) compared with controls. AVR led to regression of LV hypertrophy with LV mass that was no longer different from controls ( P =0.32). Nevertheless, post‐AVR patients displayed a persistent adverse morpho‐functional phenotype characterized by persistently lower velocity (mean, 0.24 versus 0.28 m/s; P =0.003) and vorticity (17.1 versus 21.1 radians; P <0.001) compared with controls. Conclusions Patients with severe AS display adverse prothrombotic LA flow characteristics that persist after successful AVR despite general regression of LV hypertrophy.