We report a case of a 25-year-old man diagnosed with an unusual case of cor triatriatum sinister with a mobile left atrial thrombus. He was hospitalised with aggravating dyspnoea. Transthoracic echocardiography revealed a membrane-like structure traversing the left atrial and a small orifice of about 7.1 mm. The mean pressure gradient was 12.94 mmHg across the orifice of the membrane-like structure and there was a mobile mass in the post-erosuperior chamber. The anomaly was rectified by a surgical resection. Timely diagnosis and surgical repair may prevent stroke in patients with unusual cor triatriatum sinister. © The Author(s), 2020. Published by Cambridge University Press.