Numerical analysis was performed on the enzyme transport and the flow fields in order to predict the effectiveness of urokinase injection regimens in clot dissolution. The species and momentum transport equations were numerically solved for the case of uniform perfusion of enzyme into a fibrin clot for an arterial thrombus and a deep vein thrombus models. In order to predict the thrombus lysis efficiency of continuous and forced intermittent injections, enzyme perfusion and clot lysis were simulated for the different injection velocities. Intermittent injection showed faster clot lysis compared to continuous perfusion, and lysis efficiency was increased as injection velocity increased.