BACKGROUND In patients with atrial fibrillation (AF), the presence of a left atrial thrombus correlates with the highest risk of stroke. Mitral stenosis (MS) is an acquired disease that leads to atrial pressure overload and subsequent significant anatomical and electrical remodeling of the left atrium. This promotes the occurrence of AF and atrial thrombus formation. Proper anticoagulation decreases the stroke risk in AF patients. Unfortunately, there is insufficient data on the effectiveness of non-vitamin K antagonist oral anticoagulants (NOAC) in patients with AF and MS. CASE REPORT We present a case of 64-year-old woman referred for electrical cardioversion (CV) due to symptomatic AF. She was administered an apixaban for stroke prevention, but she missed the scheduled echocardiography prior to referral. Imaging performed on-site revealed a giant left atrial thrombus and moderate MS. High mobility of the intracardiac mass together with moderate AS and MS were assessed as significant predictors of distal embolization. The patient underwent mitral valve replacement with the thrombus removal. Her further recovery was uneventful. CONCLUSIONS Mitral stenosis significantly affects the anticoagulant selection in patients with atrial fibrillation. Thus, echocardiography is mandatory if the first diagnosis is atrial fibrillation to exclude contraindications for NOAC therapy.