Mitral stenosis is closely linked to atrial fibrillation and subsequent thrombus formation in the left atrial appendage (LAA), significantly increasing the risk of cardioembolic stroke. While oral anticoagulation remains the standard management strategy, persistent thrombi, bleeding complications, and patient non-compliance continue to pose challenges. We report the case of a 57-year-old woman with rheumatic mitral stenosis who presented with exertional dyspnea. Clinical examination and transthoracic echocardiography (TTE) confirmed severe mitral stenosis with a valve area of 0.7 cm² and no visible thrombus. She was scheduled for percutaneous balloon mitral valvulotomy (PBMV), but a pre-procedural transesophageal echocardiogram (TEE) identified a small left atrial thrombus (1.2 × 1.1 cm), prompting temporary deferral of the procedure. Following five days of intravenous heparin therapy, repeat TEE demonstrated a reduction in thrombus size and procedure successfully dilated mitral area to 1.5 cm² using a 25-mm Inoue balloon via a modified over-the-wire technique and no procedural complications. In this case, the thrombus demonstrated responsiveness to short-term intravenous anticoagulation and the fact it is LA thrombus type Ia which location not protrude to LA cavity, allowing safe execution of PBMV using a technique designed to minimize thrombus disruption. This case highlights that, with appropriate imaging, anticoagulation, and procedural modification, the presence of a left atrial thrombus may not constitute an absolute contraindication to PBMV.