Thrombotic stroke, which is caused by blood clot in the cerebral artery, is a major source of increased mortality and morbidity. Considering as efficient and fastest methods, mathematical approaches have gained significant importance for analyzing and understanding the biological events like thrombosis. This paper presents a computational model to analyze the effects of thrombosis using the theory of coupled fluid dynamics-structure interaction. The finite element method is used for the modeling of thrombosis (blood clot) of different stages in the middle cerebral artery with physiological compliance. The developed model is used to investigate the consequences that occur due to the various sizes of clots in the artery in the form of blood flow velocity, blood pressure, and artery wall stress. Such numerical assessment will facilitate better understanding of the biophysical process in case of thrombosis and thus would support medical practitioners to take faster curing steps.