BACKGROUND: Non-bacterial thrombotic endocarditis (NBTE) is an uncommon pathological situation, which involves the presence of bland, fibrin-platelet thrombi. It usually occurs at the endocardium of cardiac valves, in association with endothelial injury and a hypercoagulative state. However, NBTE on the endocardium at the right atrial free wall in a patient without any apparent hypercoagulative background is rarely reported. CASE PRESENTATION: A girl aged 4 years with severe pectus excavatum was referred to our hospital for treatment of a recurrent right atrial tumor. The tumor was removed concomitant with pectus excavatum repair. The tumor was revealed as recurrent thrombus. Pathological findings showed that NBTE caused by an operative scar on the endocardium of the right atrium and sustained rheological stress in the right atrium due to compression from pectus excavatum lead to recurrent thrombus formation. Three years after the discontinuation of anticoagulation therapy, no sign of thrombus formation was found. CONCLUSIONS: To our knowledge, this is the first report of NBTE related to an interaction between sustained rheological stress from cardiac compression and endocardial injury. In such patients, we recommend concomitant chest wall repair when the operative scar is present at the site of the rheological force.