Percutaneous balloon mitral valvuloplasty (PBMV) has recently become the treatment of choice for many patients suffering from mitral stenosis. In the current report, we introduce a 26-year-old woman who presented to us with palpitation and exertional dyspnea but without any remarkable medical history. ECG illustrated the sinus rhythm, transthoracic echocardiography (TTE) showed severe rheumatic mitral stenosis and (2+) mitral regurgitation, and transesophageal echocardiography (TEE) demonstrated severe mitral stenosis and no thrombus. Accordingly, the patient underwent percutaneous transvenous mitral commissurotomy (PTMC). On the following day, TTE showed a fresh mobile thrombus in the right atrium attached to the atrial septum, which was confirmed by TEE. As a result, the patient received 1 mg/kg (60 mg) of enoxaparin subcutaneously twice daily plus 5 mg of warfarin daily. Subsequent TTE revealed no mass 4 days after the treatment. Evidence suggests that endocardial surface injury and trans-septal puncture during PTMC may be associated with clot formation, which is aggravated by low blood flow in the right atrium and the catheter as a foreign body. This case report emphasizes the importance of postPTMC anticoagulant therapy.